I have questioned this specifically both to those in seminary and those out... I have questioned this with religious studies professors as well as ethics professors...
I urge you to read the bible in both the latin and hebrew context, no I do not speak either fluently, however there are some great reference books out there that provide verse to verse translation and contextual referencing which is all so important. Biblical scripture is riddled with testaments too war, the main principle you need to be concerned with is that the bible does not deal with government institutions and individuals in the same manner.
Scripture: Romans 13: 1-5, John 19:11, Matthew 8:5-10, 1 Timothy 2:1-6
In fact the bible was quite specific in the OT about the Israelites guidelines in military :
Scripture: Numbers: 1:2-4, Deuteronomy 20:5-12 & 20:19 & 23:12-13, Chronicles 25:5-6, Numbers 1:47, Samuel 30:3 & 18-19, Romans 13:1-7, 1 Samuel 30:8.
The questions of Exodus 20: 13 have already been answered in relation to the Hebrew context of murder. Unjust premeditated killing with the wrong motives of hatred, vengeance, greed, jealousy, etc. is murder. Killing in self defense to protect oneself is not murder nor is executing condemned killers. It is our civic and social duty to protect ourselves and our fellow man, God helps those that help themselves.
Historically there have been a number of prophecies that have been fulfilled during war in the name of God and prophetic vision: David, Constantine, Joan of Arc, the Knights Templar, Arch Angel Michael and his armies, and even Aquinas made a justification in his "Just War Principle".
If you have indepth questions on this issue or would like some suggested literature and reading material feel free to PM me...