First of all we need to start with Dominique's relationship to Howard, as I think your question doesn't do that full justice. Their relationship is rather complicated, from their very first encounter in the granite quarry and the infamous quasi-rape scene, over her seeming work against him while simultaneously sleeping with him, to her complete renunciation of him. It is also a relationship that is ultimately driven by the novel's core themes of individualism and how society supposedly tries to crush it. I don't quite claim to fully understand what drives all aspects of their relationship, since it is indeed a little confusing at first and laden with a lot of ideologically motivated gestures, but it doesn't just come down to a sudden realization at the end, neither for Dominique nor for Howard.
While it does seem at first that she disdains him, that is not the whole truth and in fact I would pose that they fell in love at the very first moment they saw each other in the quarry. And that is not because Dominique is an exceptionally beautiful woman, since I don't think Roark would care much about that. If anything, both their outward presences are likely a representation of their inward attitudes. It is because she ultimately shares his individualistic ideals, she just has a different way of dealing with it and the forces working against it. He sees her in a way he doesn’t see many other people.
Yes, at first the relationship does start as kind of a hate-love and their supposed control over each other is a large part of the tension that keeps it going. Their public professional antagonism is what gives their private encounters meaning. Quoting from their first night in his apartment in Part 2, Chapter 7:
"You know that I hate you, Roark. I hate you for what you are, for wanting you, for having to want you. I’m going to fight you--and I’m going to destroy you--and I tell you this as calmly as I told you that I’m a begging animal. I’m going to pray that you can’t be destroyed--I tell you this, too--even though I believe in nothing and have nothing to pray to. But I will fight to block every step you take. I will fight to tear every chance you want away from you. I will hurt you through the only thing that can hurt you--through your work. I will fight to starve you, to strangle you on the things you won’t be able to reach. I have done it to you today--and that is why I shall sleep with you tonight."
"I have hurt you today. I’ll do it again. I’ll come to you whenever I have beaten you--whenever I know that I have hurt you--and I’ll let you own me. I want to be owned, not by a lover, but by an adversary who will destroy my victory over him, not with honorable blows, but with the touch of his body on mine. That is what I want of you, Roark. That is what I am. You wanted to hear it all. You’ve heard it. What do you wish to say now?"
But it is with him that she can actually be herself. It is possible a true love only develops from that later on, but even if maybe both don't realize it at first, it is a loving relationship albeit one drenched in mutual control and pain. Yet the above passages highlight why Dominique also hates Howard. She hates him, and herself for loving him, because he is incorporating an individualistic ideal that is ultimately doomed. We already know she deeply appreciates his work. She herself hates the society of phonies that she is part of and expresses that with mockery and a cold reclusion. There is already a hint of this when we look at her criticism/praise of the Enright House in Part 2, Chapter 8:
A few days later, in his room, sitting on the edge of his drafting table, she looked at a newspaper, at her column and the lines: "I have visited the Enright construction site. I wish that in some future air raid a bomb would blast this house out of existence. It would be a worthy ending. So much better than to see it growing old and soot-stained, degraded by the family photographs, the dirty socks, the cocktail shakers and the grapefruit rinds of its inhabitants. There is not a person in New York City who should be allowed to live in this building."
Roark came to stand beside her, his legs pressed to her knees, and he looked down at the paper, smiling.
"You have Roger completely bewildered by this," he said.
"Has he read it?"
"I was in his office this morning when he read it. At first, he called you some names I’d never heard before. Then he said, Wait a minute, and he read it again, he looked up, very puzzled, but not angry at all, and he said, if you read it one way...but on the other hand..."
"What did you say?"
"Nothing. You know, Dominique, I’m very grateful, but when are you going to stop handing me all that extravagant praise? Someone else might see it. And you won’t like that."
"You know that I got it, from that first article of yours about the Enright House. You wanted me to get it. But don’t you think someone else might understand your way of doing things?"
I myself at first read it as a praise in that way and was surprised by that. Not only does that hint at her ultimately helping him with her criticism (especially when we see that in connection to her earlier meeting with Toohey where he says that he doesn't write about Roark at all in order to not give him attention and a platform). It also highlights a controversial aspect of why she wants to stop Roark, which is so that the rest of society can't crush him themselves. It is his ultimate failure that she wants to protect him, but even more so herself, from. She doesn't think him fitting into society but instead of helping him she thinks that a lost cause and wants to inhibit his success at the seed. His existence and actions worsen her pain in this society. This true attitude of hers is seen best in her sarcastic and disillusioned testimony at the Stoddard trial in Part 2, Chapter 12:
"Howard Roark built a temple to the human spirit. He saw man as strong, proud, clean, wise and fearless. He saw man as a heroic being. And he built a temple to that. A temple is a place where man is to experience exaltation. He thought that exaltation comes from the consciousness of being guiltless, of seeing the truth and achieving it, of living up to one’s highest possibility, of knowing no shame and having no cause for shame, of being able to stand naked in full sunlight. He thought that exaltation means joy and that joy is man’s birthright. He thought
that a place built as a setting for man is a sacred place...
I do not condemn Ellsworth Toohey. I condemn Howard Roark. A building, they say, must be part of its site. In what kind of world did Roark build his temple? For what kind of men? Look around you. Can you see a shrine becoming sacred by serving as a setting for Mr. Hopton Stoddard? For Mr. Ralston Holcombe? For Mr. Peter Keating? When you look at them all, do you hate Ellsworth Toohey--or do you damn Howard Roark for the unspeakable indignity which he did commit? Ellsworth Toohey is right, that temple is a sacrilege, though not in the sense he meant. I think Mr. Toohey knows that, however. When you see a man casting pearls without getting even a pork chop in return--it is not against the swine that you feel indignation. It is against the man who valued his pearls so little that he was willing to fling them into the muck and to let them become the occasion for a whole concert of grunting, transcribed by the court stenographer...
...The Stoddard Temple must be destroyed. Not to save men from it, but to save it from men. What’s the difference, however? Mr. Stoddard wins. I am in full agreement with everything that’s being done here, except for one point. I didn’t think we should be allowed to get away with that point. Let us destroy, but don’t let us pretend that we are committing an act of virtue. Let us say that we are moles and we object to mountain peaks. Or, perhaps, that we are lemmings, the animals who cannot help swimming out to self-destruction. I realize fully that at this moment I am as futile as Howard Roark. This is my Stoddard Temple--my first and my last."...
And in fact the Stoddard trial and its outcome, especially after she herself participated in the temple's aspirations to her seeming enjoyment, is the final drop for her that crushes all hope to see Howard Roark prevail in this world rather than just wasting himself to it. It is right after that that she abandons him completely and marries Peter. She just gives up. While she shares Howard's ideals, she doesn't share his indifference to the rest of the world. She hates the world for what it does to Howard and she hates Howard for having it be done to him. Yet she loves him for the man he is and can't bear to see him fail. But she sees no other way than to sacrifice herself to this world and letting herself be engulfed and punished by it, as well as cutting ties to Howard. She thinks she can only function in either extreme, embracing individualism or denouncing it. So she becomes the negating parody of the empty shells she sees walking around everywhere, married to someone she despises and not allowing herself to be happy in a world controlled by "second-handers". To quote from her ultimate surrender to Howard and the rest of the world in her final visit to him in Part 2, Chapter 14:
...Roark, I can accept anything, except what seems to be the easiest for most people: the halfway, the almost, the just-about, the in-between. They may have their justifications. I don’t know. I don’t care to inquire. I know that it is the one thing not given me to understand. When I think of what you are, I can’t accept any reality except a world of your kind. Or at least a world in which you have a fighting chance and a fight on your own terms. That does not exist. And I can’t live a life torn between that which exists--and you. [...] Am I too weak because I can’t do this? I don’t know which is the greater strength: to accept all this for you--or to love you so much that the rest is beyond acceptance. I don’t know. I love you too much."...
"You’re not aware of them. I am. I can’t help it, I love you. The contrast is too great. Roark, you won’t win, they’ll destroy you, but I won’t be there to see it happen. I will have destroyed myself first. That’s the only gesture of protest open to me. What else could I offer you? The things people sacrifice are so little. I’ll give you my marriage to Peter Keating. I’ll refuse to permit myself happiness in their world. I’ll take suffering. That will be my answer to them, and my gift to you. I shall probably never see you again. I shall try not to. But I will live for you, through every minute and every shameful act I take, I will live for you in my own way, in the only way I can."
So we can't quite brush her motivations off as disdain and running off with his rival while waking up at the end to realize who her true love is. She knows it the whole time, she just can't live with it. She is quite a controversial and tragic character in that way. It is only at the end, or rather in the course of the Cortlandt demolition, that she overcomes this hatred of the world, Howard, and herself and literally rises up to him.
And there in that heart-breaking testimony of love we also understand Howard's ongoing love for her. Not only has he found a strong individual personality in her that he can "exist against". He also understands what she does to herself and why she does it and he knows that it is necessary but ultimately will go over. He could not love her as the empty shell that she gives Peter Keating, yet he knows that she can't exist in this world in any other way and that it is a sacrifice of love she commits. But he knows that she will eventually overcome her fears and her hatred and when that finally happens, we will be there for her. So yes, I think he saw that "superwoman" in her from the getgo, only it took time to surface:
...I love you, Dominique. As selfishly as the fact that I exist. As selfishly as my lungs breathe air. I breathe for my own necessity, for the fuel of my body, for my survival. I’ve given you, not my sacrifice or my pity, but my ego and my naked need. This is the only way you can wish to be loved. This is the only way I can want you to love me. If you married me now, I would become your whole existence. But I would not want you then. You would not want yourself--and so you would not love me long. To say ’I love you’ one must know first how to say the ’I.’ The kind of surrender I could have from you now would give me nothing but an empty hulk. If I demanded it, I’d destroy you. That’s why I won’t stop you. I’ll let you go to your husband. I don’t know how I’ll live through tonight, but I will. I want you whole, as I am, as you’ll remain in the battle you’ve chosen. A battle is never selfless."...
"You must learn not to be afraid of the world. Not to be held by it as you are now. Never to be hurt by it as you were in that courtroom. I must let you learn it. I can’t help you. You must find your own way. When you have, you’ll come back to me. They won’t destroy me, Dominique. And they won’t destroy you. You’ll win, because you’ve chosen the hardest way of fighting for your freedom from the world. I’ll wait for you. I love you. I’m saying this now for all the years we’ll have to wait. I love you, Dominique."
So to some degree maybe it is a bit like you write in your own story that you compare it with. Howard sees something in Dominique that maybe she doesn't fully see herself or can’t accept. He sees the bigger person she is bound to be, accepting that she can't yet realize that herself.