Let's not forget the really offensive place the metaphor breaks down: Mutants make it very clear that THEY'RE NOT HUMAN BEINGS. Ultimatum actually corrected that and made the metaphor a bit better by saying that mutants are no more than human-made, altered HUMANS. But as the main version of the X-Men stands, are we to then think, well, then we're supposed to be tolerant of blacks and gays in spite of their not being human?
Of course they are human, and it's offensive to use mutants as an analogy therefore. It also seems to have been a convenient way to use the N-word: twice Claremont had Kitty, specifically, take the word "mutie" as an excuse to use the N-word, once in "God Loves Man Kills" and another in a story quoted on another recent thread(though that bit isn't included).
Now, granted, Kitty's a white girl from the Chicago suburbs and probably has no problem using that word anyway. I have always assumed she was at least a light racist, one reason I've never liked her. Shame that was never delved into, why she leaps to that word so easily. Or why Claremont does.
But it's offensive. Black people are real. Mutants are not. At that point the analogy becomes a little tangled and insane.