The thing is, Autumn's goal after rebelling is to get Project Purity up and running, so he can give water to the wastelanders. Or at least, that's all I am able to infer. If that is his goal, why the hell does he come in and try to take over the whole thing himself? If he really is such a good guy, he should have left well enough alone, or at least offered to help protect all the scientists working to make the project a reality. Instead, he breaks in, kills people, and gives them every reason to distrust him and not want to help him. If nothing else, that makes him a stupid and inefficient good guy, and still worse off than we were before.