… you are not going to stop short of ending the threat. If you factor in the adrenaline flowing in the good guy and the perp, a wound to the leg or knee isn’t going to necessarily make them drop the gun. Even if they do, they can still grab it and shoot you.
I believe normal protocol in an officer involved shooting is to suspend them until after the investigation. I don’t think JJ did anything wrong, but Abe will never see it that way being Theo’s father.