Stanley Hauerwas' short article "Why Homosexuals (as a Group) are More Moral than Christians (as a Group)", written during debates surrounding admitting homosexuals into the military, made a great point - the real debate should be over whether to let Christians in. True ones make dismal soldiers. He could have gone much further.
First, the more Christian soldiers espouse just war theory, the more likely they may begin thinking through what they mean by it. Sooner or later protecting oil fields or killing Muslims is going to come up short. What are you going to do with a massive standing army who keeps asking, Should we be doing this?
Second, if a soldier obeys orders and kills civilians there's the nasty business of church discipline, handing them over to Satan. That's terrible for morale.
Third, Christians will (counter-intuitively) pray for their enemies. They will demonstrate mercy over justice. They will turn the other cheek. In fact, they may get confused and accidentally do corporately what they vigorously practice privately. Or they might just realize that's a stupid distinction anyway.
Fourth, they share a commission greater than capitalism. What happens when they begin to lose gospel credibility because they keep shooting everybody? They might be forced to choose baptizing over bombing, witnessing over water boarding.
Finally, Christian soldiers are ultimately under not the commander in chief but Christ. And worse, they are striving to become more and more like him. Which means they are becoming decidedly less and less what they are defending. Old wine skins can't hold the new wine.