The issue is whether you can shoot an ARMED assailant who has made a threat on your life, at a time when it is advantageous to YOU, ie when his back is turned or he is occupied with stealing your vehicle. As you are presumably right there next to him, your life is still in danger, as is anyone else nearby. Also, assuming the vehicle is loaded with firearms, you can make a case that you were trying to prevent a much more serious crime down the road. I believe that many states have provisions covering you for using deadly force to prevent a felony you know will be happening (ie, a guy robs you, then says he is going to go rape someone else), or who has dsiplayed homicidal behavior in the past and can be presumed to do so in the future (a felon making multiple car jacks during a high speed chase, by you shooting him, you are possibly saving the life of his next car jack victim).
Anyway, it probably all comes down to the DA in your area, and whether or not you gave a verbal warning to the crooks. Sneaking up on the guy and assasinating him with a shot to the back of the head won't look good (to a jury 6 months after the fact anyway). Calling on him to drop his weapon and get out of the car, then shooting him if he doesn't respond immediately, isn't much different IMHO, though the police might see it that way, especially if you were protecting dangerous/valuable cargo (firearms, explosives, kids, etc).
Ugh, if only Texas had open carry, range trips would be SO much easier!