This is an exact reason why I couldn't be in the military, regardless of how much I want to serve my country and show some honor. I just have that conviction. Others may not. It's a shady area, but I've always taken it literally from the original KJV.
(Thinking out loud here) Although if you want to take it that literal, "Thou shalt not kill" should also mean you cannot kill a chicken/pig/deer/goat/steer/cow/lamb etc, even if it is for food. Yet the killing of animals for food is not condemned and sacraficing lambs in the old testament jewish religion is even a nescessity to pay for the debts of sin. This is also the exact same reason Jesus Christ gave himself to die. Thus killing in that context is not only permited, but it's condoned throughout biblicle scriptures.
The BIGGEST thing is the distinction between "murder" and "killing". From what I've read, in the original Jewish text it used the word "murder". However somewhere along the translations the word "kill" was used instead.
Farthermore to the question at hand: I saw a website once that explained that there is a difference in a war between nations, and cold blooded murder. It cited some examples from the old testament, but the only example that I really remember was the one where they wrote about where in the New Testament is speaks of Christ acknowleging a Roman Centurion and recieved him. They used this to suggest that God does not judge one for having a military occupation, but that it is an honorable occupaton and with regard to war, they went on to use this passage...
1 Timothy 2:1-2
2:1 I urge, then, first of all, that requests, prayers, intercession and thanksgiving be made for everyone- 2 for kings and all those in authority, that we may live peaceful and quiet lives in all godliness and holiness. (NIV)
I personally hate the thought of war, killing of men and women of other nations, but within the framework of God's own ordinance that governments exists by his will, the preservation of that nation will sometimes necessitate war in order to provide security for its citizens.
Praetorians in the Roman army were also converted to Christianity by the Apostle Paul, yet there is never any indication they ever changed their occupation, nor were asked to. Cornelius, a centurion, is the first mentioned when this occured.
As a side note I did a google search to try and find it and instead I found this
interesting article about scripture and war.