Perhaps if you made some of the NPCs Militaristic and Friendly as long as you dont shoot at them? Such as a Military patrol that clears out zombies from time to time when they come across them but wont open up on the player so long as you dont open up on them. If you do open up on them, all the AI NPCs will deem you hostile. They would also give you 2 chances to not open up on them. AKA you could kill up to 2 of them (each time a message displays to stop killing friendly AI) after which a message would display that all the NPCs are gunning for you. And then all the NPCs hunt you. Also, some NPCs would just be hostile in general. They could also attack the friendly AI patrols too.