The point of Fallout was there was rarely any "good" people, apart from the vault dweller...if you choose them to be.

That's what makes the shade of grey BoS more fun as most of the time you can change them. Making your actions have more of an impact.

Only exception is Fallout 4 I believe where there is a secret ending you can do where they all get on but I believe it's more of a "Genocide on hold." Than anything else. It's been a long time since I played fallout 4 so could be wrong.