I do agree that there should have been a lot more of a "this is a bad thing" vibe about how they took out bucket-head, like sort of a low-scale version of using the atom bomb. It's a big deal, even if it's the only way (a friend of mine I saw it with, who is apparently more bloodthirsty than I thought she was, wanted to know why Beast didn't just stab him in the throat. Even a decent kick to the back of the head should have been able to knock him out).
All the "cured" mutants will get their powers back later, anyway, if/when they make more. Even if they have to resort to the plot-device machine from the first movie to do it.