In NYC and NJ (work, live) it's self protection first. If the entrance wound is in the front and he's armed with say, a butcher knife from your kitchen drawer (not trying to give you ideas but....), then your pretty safe from a charge. BUT, if it's a handgun, they'll still go after you in NYC for possession, probably be OK in Jersey if it's registered.
It works best if the thief can't talk anymore. If he can still talk, he can cause a problem. Nervious home owners can be excused for firing more than one shot.
As a general rule, cops don't like invaders either. If your clearly in the right they'll pretty much take care of it in the language of the police report (I used to be a local cop).
Al