Jay, something that you might not have been clear on in all that confusion that changes things here is what the man's powers were. He apparently fed off... support, for lack of a better word. SHIELD will have to be the ones to determine precisely how it works.

But the thing is, the people who were attacking Apocalypse weren't doing it for the fun of it. They were doing it because that was precisely what was necessary to counter his power. Even the people who weren't actually physically attacking him were... rejecting him. It was literally the only way we knew of at the time to depower the man.

I don't know where this perception came from - not just you - that it was done out of vengeance. It wasn't. It was a tactical necessity - whatever emotional overtones were there, they were secondary.