There's definitely an argument made that you can interpret it that way, and I think there's good reason too. From the lyrics, there seems to be an emphasis of "my way or the highway" sort of mentality with Elphaba, and her her yearning for independence if it means freedom and truth is reflected numerously in this song. For example, at the beginning of the song, Glenda says to Elphaba:

Listen to me! Just say you're sorry!
You can still be with the Wizard

Which she replies back,

I know
But I don't want it - no!
I can't want it anymore.

This is further elaborated a bit later in the song where she goes

Too long I've been afraid of
Losing love, I guess I've lost
Well if that's love
It comes at much too high a cost

She encourages Glenda to join her in her quest, in which Glenda hesitates and decides to stay behind, which is the reason why Elphaba says

If I'm flying solo, at least I'm flying free

Meaning although she's going to be alone in this, she is completely independent of what anybody else tells her to do.

So what about the "so low" part? In order to understand this, you need to go back to the song that comes before it, titled "Sentimental Man". It's sung by the Wizard, and it's pretty short. It goes like this:

I am a sentimental man
Who always longed to be a father
That's why I do the best I can
To treat each citizen of Oz as son or daughter
So Elphaba, I'd like to raise you high
'Cause I think everyone deserves the chance to fly
And helping you with your ascent allows
Me to feel so parental
For I am a sentimental man.

Now look at this line again:

So Elphaba, I'd like to raise you high,
'Cause I think you deserve a chance to fly
And helping you with your ascent....

Oz is saying in the previous song about how he's going to use his influence and power to raise Elphaba's stature. But in the events which follow after, Elphaba discovers that Oz is a fraud. This makes Elphaba echo Oz's own words back when she sings,

As someone told me lately
"Everyone deserves the chance to fly"

She uses Oz's own words back at him, saying, "Yeah, that's right, 'everyone deserves a chance to fly', and I'm going to use that chance!"

I don't think it's any coincidence that the line directly after "everyone deserves the chance to fly" is

And if I'm flying solo
At least I'm flying free.

So in one sense, she's saying "I'm doing this by myself, but at least you (i.e. Oz), aren't telling me what to do." On the other hand, she's rejecting Oz's offer to "raise her high", and saying, "even if I'm flying so low, at least I'm doing it on my own." She's acknowledging the risks that come with defying the wizard (tarnished reputation, being hunted, etc.) and saying "Screw that clout". This is modeled perfectly by Elphaba says to Glenda,

I hope you're happy too
I hope you're proud how you Would grovel in submission To feed your own ambition

Throughout the entire musical, Elphaba and Glenda are considered foils. Glenda is one who follows the rules and is willing to conform to progress in her status, while Elphaba is willing to break those even if it means her stature or how other people view her.

I hope this helps!