The comparison of HoM to actual genocide seems to stem from the continued use of the X-men metaphor as if it were realistic. But mutants can never really be like real minorities. Ironic considering Scarlet Witch is an actual minority, a Romani woman (although she doesn't seem to always be portrayed as one), and experienced real prejudice in her life, unlike Cyclops or Angel.
Also, the entire concept was just to keep the mutant minority thing going anyway, which is something many fans seem to hold onto, yet seems to the reason for HoM in the first place. Why couldn't Marvel just let mutants grow in number and be happy, and not fight everyone while pretending to be real minorities?