Agent Z put a bullet in this one's face, then double-tapped the corpse, then nuked it from orbit just to be safe, but I'll just say this: The Mutant metaphor is stupid. It has always been stupid. It will always be stupid. It can't be fixed. Good science-fiction and fantasy allows for parallels, but it doesn't make the mistake of directly comparing itself to its object of criticism. Imagine how much worse that episode of classic Trek would have been, if Captain Kirk turned to face the audience and said: "It's just like Jim Crow, you guys."
But Chris Claremont be like, "Naaaaah, Magneto was in the Holocaust. MUTANT METAPHOR!"