That same goal could've easily been accomplished without the karma system. In fact, blindly accepting what the game thinks is good and bad just makes it worse.
I killed the ghouls, too. Didn't kill the ones who weren't part of the mudering, though, just Roy and the guy who attacked me. The game considered it "bad karma". How? Why is killing that guy bad karma, but shooting Tenpenny in the face, often with no reason, mind you, is quite alright.
You can't foresee the motivations of players' actions with a simple karma system. Life doesn't work like that. Sure, there are things that are monumentaly good and bad - but in a world like Fallout 3, even those get all mashed up. Grading certain actions with a karma system is not only limiting creative thinking, not only disconnecting the player with the character, but if you give rewards based on it, that limits the player's freedom. In a game like Fallout 3, that's fucking unacceptable.