I don't think this film is meant to be a Civil Rights Allegory.
I believe the comic books first took on a sort of Civil Rights tone, but the more recent movies seem to have taken on a tone of being about homosexuality rights than rights for minorities or women.
For example, Magneto tells Mystique that she's working too hard to hide who she "really is" and she needs to be herself. Pretty much a clear allegory to gay people working too hard to stay in the closet when they shouldn't have too.
This similarity is perhaps most clear in the second X-Men movie when Iceman's mother says to him, "Have you tried
not being a mutant?"
And, of course, Bryan Singer himself is gay so it would seem to follow the X-Men movies under his watch would take on such a tone.