also, astonishing x-men was not nearly the first time a "cure" for mutations was part of a comic's plot. anti-mutant activist groups have been attempting to make cures for mutations since the first days of the x-men. and why would apocalypse want to "cure" mutants, being that he's a darwinist madman who believes mutants are all that's fit to inherit the earth. and not even ALL mutants at that.
the movie, i'd bet, probably isn't taking its cues directly from a comic plot. "the cure" has been a recurring theme over the decades, but i doubt it'll be done in X3 in a way it's been done on-panel. also, i highly doubt they'd pick the ord-heavy version from astonishing, for the simple fact that involving aliens is probably higher on their "keep away" list than actual continuity.