Superman kills Zod. Big whoop. Yes, I know he's not a killer by nature. But when Superman realized that there was no other way to stop Zod without everyone else on Earth being endangered mortally, well.....needs of the many.
Superman screamed in angst when he was forced to kill Zod. Not only was he forced to kill, to break his prime principle to save the world, but he was forced to kill a fellow last survivor of Krypton. (essentially, a brother) It's not like he's going to turn into a habitual killer.
A pacifist may one day actually be forced to fight.....and he/she might deeply regret having done so....but if it was to save the life of a friend or loved one, it does not mean they've given up on their pacifism. It meant doing the right thing regardless of how they hold theirselves, and such a person may hope/pray that they never have to do something so distasteful, so disturbing, again in their life time.