The Time books use a lot of Christian imagery, so there is probably also an explanation in terms of religious parallels, but for this answer I've adopted a purely character-based interpretation.
Meg's point of view of the world has evolved; the contradiction represents her two different perspectives
In A Wrinkle in Time, Meg felt out of place in the world. She didn't seem to fit in with her peers. Her teachers didn't seem to understand her. She was uncertain about her future, and lashed out with sarcasm and copious self-loathing. We can see this from this passage early in A Wrinkle in Time:
School. School was all wrong. She’d been dropped down to the lowest section in her grade. That morning one of her teachers had said crossly, “Really, Meg, I don’t understand how a child with parents as brilliant as yours are supposed to be can be such a poor student. If you don’t manage to do a little better you’ll have to stay back next year.”
During lunch she’d rough-housed a little to try to make herself feel better, and one of the girls said scornfully, “After all, Meg, we aren’t grammar-school kids anymore. Why do you always act like such a baby?”
And on the way home from school, walking up the road with her arms full of books, one of the boys had said something about her “dumb baby brother.” At this she’d thrown the books on the side of the road and tackled him with every ounce of strength she had, and arrived home with her blouse torn and a big bruise under one eye.
— A Wrinkle in Time, pp. 3–4. Kindle Edition.
Camazotz represented Meg's view of her world at the time, a place where she was penalized on math exams for using a different method to solve the problems even though it resulted in the same answer. Meg felt she was being persecuted, cruelly forced to conform to an unjust order imposed on her by a higher power. Her adventure on Camazotz let her struggle against that injustice symbolically. Entering IT's room and doing battle with IT, and defeating it with her love for her brother Charles Wallace, who is also a misfit under the current order of the world, was an act of rebellion, an act of destruction that symbolized what Meg wished to do to the order of her life back on Earth.
By the time of A Wind in the Door, Meg is feeling much more secure and having an easier time fitting in. Her mother points this out early in Chapter 2, and Meg responds that getting close to Calvin has helped her fit in more because of how well regarded Calvin is at the school. Meg is still uncertain about her future, but she's much more positive about it; she even asks her mother if she'll ever be a double PhD like her mother is, implying that she's given some thought to where she might want to go in life.
Charles Wallace is the one who suffers for being different in A Wind in the Door, but unlike Meg in A Wrinkle in Time, who angrily rebelled and castigated herself for being unable to fit in, Charles Wallace is trying to find a way to adjust his own behavior and peacefully get his classmates to accept him. When discussing the subject in Chapter 3, Charles says "What I really need are lessons in adaptation. I’ve been reading Darwin, but he hasn’t helped me much." Meg tries appealing to a higher power on Charles's behalf, and goes to talk with her old enemy Mr. Jenkins, the principal of her school in Wrinkle and now the principal of Charles Wallace's school in Wind. This fails, but it shows how Meg has matured: instead of reacting with violence and rebelling, she tries to solve problems with diplomacy, and she does so on behalf of another person instead of for her own benefit.
The universal order in A Wind in the Door springs from a recognition that everything in the universe is interconnected. As the cherubim Proginoskes puts it in Chapter 11, "[W]e all need each other. Every atom in the universe is dependent on every other." The farandolae are meant to Deepen, transform into tree-like farae, and take their place in the cosmic order, singing the song of creation alongside the stars. Fearful of growing up, some of them refuse to Deepen and reject the idea that everything is interconnected, but this rebellion, unlike Meg's against IT, is not noble; instead it plays into the hands of the Echthroi, creatures who want to negate all of existence. Meg and her allies must convince Sporos, one of the wayward farandolae, to stop rebelling, to stop fearing growing up, and play his "indispensable part" in "the great plan", take his "own unique share in the freedom of creation". (Chapter 11, p. 219.)
The nobility of conforming, of taking one's place in the cosmic order in A Wind in the Door, symbolizes Meg's new perspective on her life. Now Meg feels that she has a place in society. She cares for other people, like Calvin and Charles Wallace, more than herself. She is learning to see others' perspectives, most dramatically in Chapters 5 and 6 when she has to choose the real Mr. Jenkins from among a group of imposters by learning to understand him. She has come to see the complexity of life, sighing, “I wish life didn’t have to be so complicated." (Chapter 2, p. 35). Meg now sees conforming and taking her place in society as a duty that carries both hardship and privileges, as a farandola Deepening into a fara can no longer move, but gains other abilities in return. As the fara Senex puts it:
Now that I am rooted I am no longer limited by motion. Now I may move anywhere in the universe. I sing with the stars. I dance with the galaxies. I share in the joy—and in the grief. We farae must have our part in the rhythm of the mitochondria, or we cannot be. If we cannot be, then we are not.
– A Wind in the Door Chapter 11, pp. 216-217. Kindle Edition.
"The temptation for farandola or for man or for star is to stay an immature pleasure-seeker" (Chapter 10, p. 203), but growing up, though it includes its share in the grief, also includes its share in the joy, its privileges that an immature pleasure-seeker cannot have. Meg understands this now that she's become more mature: conforming to the system takes away some of her scope to be different, but it allows her to stay with Calvin, and to go off to college and find a fulfilling career like her parents have done.