I don't get it. Why would a headshot be negative for building up karma bombs?
Headshots get you negative Karma, because they kill foes. Leg shots give you positive Karma because they subdue foes.
When evil, your kill streak is what builds up your Karma bomb.
When good, your subdue streak is what builds up your Karma bomb. If he had headshot that guy, it would have reset that little bomb counter in the upper left to zero, and he'd have to start his karma streak over.
At first I was cold to the idea, but I think, in the end, it will require you to be more skillful when playing as Good Delsin.