Caim ends up thinking he saved the world, but actually doomed humans in both timelines.
Zero was stopping the weed. Not only did she have to murder her "sisters" for that, but she also kind of fucked it up, leading to the events of the first game.
Normally when I think villain, I'm thinking someone were the events of the world would have been better if they didn't exist.
I don't recall if Caim running off would have made the word a better place. I saw he killed the boss and gave humanity time to start the Gestalt project. Now Nier is totally the villain here. Both versions of himself are dumb dumbs.
At the very least Zero tried to clean up the mess cause if she did nothing the world was doomed anyway.
I think it's pretty safe to assume that without Caim there would be no dragons and flower in the first timeline and no maso in the second one. At least people in the second one would survive until the alien invasion. If they fought back successfully, people in both timelines would survive just fine.