I helped write the movie and can tell you the gay rights/post-Holocaust Jewish identity/civil rights allegory stuff was all put in there on purpose.
Joss Whedon designed the whole ‘Cure’ storyline in the comic books specifically as a gay allegory, and Bryan Singer wove his own feelings of outsiderdom as a gay man into the movie series.
The whole ‘have you ever tried NOT being a mutant’ coming out scene in X2 isn’t even particularly subtle, while it is effective.
— X-Men: First Class screenwriter Zack Stentz confirmed on a comment thread what the tight leather costumes have been hinting at for years.
Previously: Did All the Gay Talk Hurt X-Men’s Box Office?