I don't know. I'm not gay, but I am a survivor; yet still, I can't get to upset over this.
I remember watching a movie called "Stand and Deliver". The topic of racism, amongst other things, figures into the movie. At one point, one of the characters says, "There's two kinds of racism: singling out a person because he's a minority, and NOT singling out a person because he's a minority".
This is pertinent, I think, because although gay people are often lampooned by Hollywood, this is the first and only instance I can ever recall of a gay person actually being depicted as a "villain". Perhaps there are others - but I would not say that "gay people being stereotyped as evil by Hollywood" is something that happens often enough to be a concern. Gay people are typically depicted as comic relief. I'd be more concerned about -that-. Hollywood is only starting to include gay characters in other, more complex roles, and I think that's good. The antagonist - the Head Villain - is a very complex role in a well-made film.
I watched the X-Files occasionally when it ran on TV; I never had a problem with it. I only had a problem with the majority of its fan base, which takes the subject matter depicted on the show entirely too seriously. Maybe that's why my favorite episode of the show is one in which the show is essentially making fun of itself.
But no, I don't believe this movie will make people think of homosexuals as villains, and I don't think it will make people think that abuse victims are destined to become evil disembodied heads.