Given the logistics of WW2, I'd be nervous or actually angry to have a guy like Doss in my platoon. Now, today, things are different and there are far more jobs to do in the military, but you still have to go through basic training.
If you are on the ground in Iraq and you don't believe in killing, and you would absolutely not kill a crazy ISIS cultist if he had us pinned down just to show that you believe rightly in God and he doesn't, then I wouldn't want you near me. No, you shouldn't like killing. But if that's your stance, you have other jobs available to you, including not being in the military at all as long as there's no draft or military requirement.
That's why this is infuriating.