Using your logic, we'd say, "Stopping Hitler, Good Stalin!"
Just because Stalin was necessary at a certain juncture in history to stop a greater threat doesn't mean he wasn't a cold blooded murderer who's frying in hell.
Pinochet is similar. I don't know enough about the complexities of the situation, but I think it's safe to say that even if he was necessary for a certain amount of time, he's a murderer and an evil man.
Yeah, Mother Theresa should have stopped the Commies.