You are quite correct, your conscience does bother you after killing another person and maybe it's not the right thing to do but I don't see any other way to attain peace. Maybe we will have peace if we do things Jesus way, but sometimes you have to do what you have to do.
My mom always told me if you are praying why worry and if your are worrying why pray. In essence she was saying if you are going to take things into your own hands and solve your own problem why pray to God for anything? The reality is faith and violence cannot mix. If one believes in God then they would not deliberately pick up a gun and train to kill another person. God has commissioned may wars in the past for his own reasons but today he never commissioned anyone to go to war. Those that go to war are making a decision that is independent to his directive for Christians today. God made the powerful sun, the moon and stars. He parted the Red Sea and made powerful planets in the galaxy, do you really think God lacks the power to bring about peace without humans going to war?
I never thought of it that way. I always thought those conscientious objectors and some pacifists were crazy. But I understand the logic behind the stand that they take regarding wars. I'm glad we could sit and have this conversation. Maybe we can talk a bit more about the Bible sometime.