(Before you read this, you might want to jump in and read my People’s History of the Marvel Universe series…)
That’s a fair argument, especially when the characters that are standing in as metaphors are (in their civilian clothes, and it’s noticeable that all the original X-Men could pass) five WASPY teenagers (with only one woman to boot) who live in a private boarding school in Westchester that’s run by one eccentric millionaire.

At the same time, there are a couple ways to deal with this: the first is Chris Claremont’s strategy, which is to make your cast more diverse so that you have characters who are black and mutant, gay and mutant, and so on. Thus, rather than the metaphor supplanting or erasing the thing it’s supposed to stand in for, you can explore interesting questions of intersectionality, passing privilege (see: the Morlocks), etc.
Another strategy is to have the issue of mutant rights actually interact with these other movements and politics. We see a little of this when we get into Magneto’s fascinating role in the Cold War, but I’d love to see more, especially in the original period setting. How would the black power movement of the 1970s have reacted to Storm suddenly appearing as the most powerful black woman in America? How would San Francisco politics have changed with the X-Men spending some time as the city’s super-hero team? Why don’t we see mutant urban enclaves (again, other than the Morlocks) before Grant Morrison’s run on X-Men, and how would those enclaves have fit in the complex urban politics of the 1970s? Why don’t we see a mutant rights movement, and how would that movement have developed relationships with the gay rights movement or the civil rights movement or the labor movement?
