Conflicted with the military

Looking for some insight or help. I'm religious so please don't judge. My husband is currently in the military. His service will be complete in 6 months. He doesn't know is he should re-in list. His grew up an army brat and it's the only life he really knows. However he's conflicted because of his belief. While overseas he did things and saw things that were completely against god. How can he support an army that kills innocent people. Obviously we are fighting a war and defending ourselves from terrorists, but we are atill breaking Gods commandment. His father will probably disown us if we leave. We have spoken to the pastor here on base but he's military and obviously wants us to stay. What do we do?? He cries every night thinking he's going to end up in hell.