The fact that there are mutants who would greatly benefit from power inhibitors or a suppression medicine, because of having powers that they either can't controll (yet) or which are harmfull to their physical and mental health often seem to clash with the general presentation of the mutant metaphor as being reflective of various real world minority groups including those which at some point or another suffered from attempts to "cure", "educate" or "correct" them.
As such the black and white presentation of the subject will usualy dominante. Which means that if a mutant doesn't want their powers at all or anymore, even if they are deeply harmfull to their well being, it will often be presented as either being misguided or downright wrong. Which can carry it's own unfortunate implications.
Because the more likely comparison the writer or reader could make, will be those attempts at erasing or suppressing the above alluded to minority groups in the past, rather than to situations where people have medical conditions or disabilities.
Of course this does not exclude that mutant power inhibitors or suppressors are also easily used and abused against them, which further pushes them towards being presented and perceived as bad.