The only friendly NPCs in the game which appear outside of cutscenes are Spider and the scientists.
You can't actively kill Spider. When you shoot him he flinches, but he doesn't lose health. The only way for him to die is through enemy fire. When he dies this way, it's a non-standard game over.
When you shoot the scientists you get the "Protect the innocent" warning, but you can kill them without facing any consequences (negative or positive).
An exception are the hostage scientists during rescue missions. These must not die before all the soldiers in the mission zone are eliminated and you spoke with them. Should they get killed (either by you or by a soldier), the mission restarts. But when the mission is over they count as normal scientists and can be killed.