There is a difference between Superheroes who are minor minority metaphor and telling superheroes stories with in the context of a minority metaphor . The X-men began as the first thing then turned into second thing. Oppression and Discrimination are PART of the X-men story, Oppression and Discrimination are not THE X-men story.
Chris Claremont made a smart move when he tied in real world issues into X-men dna but heavy handed trying to keep X-men as oppressed minority has lead to worse moves in the franchise. Yes the MCU should move away from being a heavily minority metaphor because many fans don't want to face repercussion of the actions take by humans in the fiction. They want seem to want this bright optimistic view coexistence in the face of mutant race destruction.