the others have already advised you a bundle of good pointers, but here's my take.
Correct me if I'm wrong, but I guess your imaginary situation would have been something like this:
The perp is alone and armed...
He can shoot back at you if you miss or fail to incapacitate him...
You''ve seen him harm others already or has clearly run amuck and could harm you, otherwise you couldn't have ascertained 'clear and present' danger or have concluded the guy's indeed a criminal...
There is no escape except if you shoot your way out (ala Emilio Estevez in "Young Guns")...
The perp has no idea you're armed and is unaware you're about to take him out...
Aaaarrrgghhhh!!! My head hurts trying to imagine...
Shoot him in the ass. So that every time he takes a dump, he'll remember his transgressions and then some. If that ain't punishment, I don't know what is.
But seriously, there's a very good chance that your bullet will hit his pelvis and he'd definitely collapse like a stack of cards. The commotion can provide you and the others with a window to escape and call the police. He'll be in a hell of a lot of pain, immobilized, and probably die of blood poisoning if left unattended.
You'll end up having a clear conscience, eh?