I am a graduate student and I believe I was discriminated against by my department. [...]Has anyone here filed a discrimination complaint against their university? Should I expect retaliation? How can I protect myself?
I'm very sorry to hear about your situation. I have been in a vaguely analogous situation, and a close relative of mine was in a more similar situation, sued, and won a settlement. My own situation was not about discrimination (I was not part of any legally protected class), but my relative's was.
One thing that isn't really clear from your question is what kind of graduate school you're in. If you're in grad school and hoping to become a dentist, then that's one situation. If you're in grad school and hoping to become a research scientist, that's different.
If it's something like the latter, then I hate to say this, but I think the reality is that if you do this, you are burning your bridges. Academia is a very small world, and finding a path to a permanent job is difficult. Even a very subtle whispering campaign can completely torpedo your chances. It doesn't even need to be a whisper. People can simply provide one-line letters of reference that don't say anything positive or negative. It's especially problematic that you describe the discrimination as being perpetrated "by my department." This means that you have zero institutional support going forward.
You may want to think in terms of choosing an entirely different life path, and not accepting any settlement that is too small to reflect the seriousness of this change in your life.
Of course, I know nothing about your situation beyond the sketch you provided, so this could be totally wrong.