I think when it comes to anti-heroes and redemptions, one of the important things you have to do is to make sure that the character in question doesn't cross a moral event horizon. Essentially, they can't do anything that the audience would consider unforgivable, if you want them to be sympathetic and/or redeemable. Since everyone has different ideas of what is and isn't redeemable, this can be a bit of a grey area, but there are a few different actions that will almost certainly push a character over the moral event horizon, like the killing of innocents or sexual assault. Since you haven't yet decided what actions your character takes, you've got a good degree of flexibility here. Some potential villainous actions that many might nonetheless sympathetic would most likely be focused on retribution, like taking revenge on the people who scorned her (but not on innocents!). I'm not personally sympathetic to revenge stories myself, but a hell of a lot of people are.
I think the main thing you should keep in mind is that in real life, most if not all trans people experience varying degrees of discrimination and oppression...and yet they do not become evil because of it. So I guess just be thoughtful. Definitely make her sympathetic if you're linking her villainy to her experiences as a trans person. But know that it's a very touchy subject that has ties to a lot of real people's trauma, and be careful. If the hero is also trans, and they approach her with empathy and understanding, I think that could go a long way.
(Weird technical tidbit: I don't see why the antlers would be an abnormally large issue? IRL they grow about five months out of the year, and she could just keep filing them down Hellboy style. In real life, many trans women shave regularly; I think it'd be a similar analogy. Inconvienient, but not unmanageable.)