I'm in the military and also a minister and I have conflicting thoughts on this subject! I was active duty for 8 years, now I'm a Reservist. While active, I spent several years in intelligence, imagery to be specific. So I have had the unfortunate pleasure of watching enemy combatants killed and allied troops fired upon.
They way I look at the profession of arms, is that it's necessary. The bloodshed that comes from violence is not pleasurable, yet there are evil people in this world that need to be removed. However, I don't agree with praying that these people die. I rather pray that they are able to find the love of Jesus before it's too late for them. You know, love your enemy and all that (Matt 5:44). Let me tell you, when you wear a uniform and see your brothers in arms being shot at and innocent people tortured and killed, its very very hard to love and pray for your enemy.
It's my belief that it is 100% ok and Biblical to pray for the safety of our troops. I have heard prayers led from the pulpit for things like the destruction of our nation's enemies, and for a group of people to be eradicated from the earth. Yes, I have heard these things. It's one thing to pray for the safety of human beings, but its whole other thing to pray for the death of human beings whose souls obviously have not been saved and will die spiritually for eternity if they die in that state.
To answer your question with a non-answer: I, as a member of the military, want to pray for victory and have my brothers and sisters come home. But as a Christian, I want to pray for all those who are innocent and affected because of the evil that is being perpetrated. And pray for the enemies of Christianity that they somehow find themselves in a position to learn and obey the gospel.