Well, I'm not an expert on the best way to kill people so...head/chest/whatever's best.
I would not try to simply cripple the assailant to keep them from coming closer (ESPECIALLY if he has a gun), because they'd still be dangerous. I'm just saying that if the situation ever did arise and I had a gun on me, I'd shoot to kill.
Don't turn this around though. If I did shoot the person causing them to lose consciousness, I'd remove all possible weapons from their vicinity, tie them or disable them from moving somehow with w/e is available, and call 911. I wouldn't just stand over their motionless body and riddle them further to ensure they are dead.
What you would do if the assailant went unconscious is not the point I am trying to make; what I am saying is that if you are put in that situation you will most likely panic and hesitate to shoot.
Think of it like this. Some time ago (not sure when, couldn't find it on Google, but we talked about this experiment in one of my classes at school) personnel responsible for turning the launch keys for ICBMs were ordered to launch the missiles because there was a nuclear attack bound for the US from Russia, and iirc like 60 to 70 percent of the key turners had mental breakdowns because they couldn't stand the thought of being the ones who turned the key to a missile that killed tens of thousands of people, and ended up not fulfilling their responsibilities.
The question is not what someone is trained to do, the question is how will they really react to a situation where they actually have to use their training. In the case of ending a life, it can be very traumatizing and most people, even soldiers, have a hard time getting through the fact that they actually killed someone.