Theological Struggle

I am having a little bit of a theological struggle. I was reading this morning in the book of Numbers, Numbers 31:17 to be exact. To set the context, Moses and the children of Israel are at camped by the Jordan River. God commands Moses to send the Israelites into battle against Midian because Midian had sought to curse and defeat Israel on their journey to the promised land. The Midianite women had also sought to seduce the men of Israel, and in doing so to sway them from worshipping God to worshipping false gods. Israel's army goes and completely destroys the Midianites, and the army carries the women and children of Midian back to the Israelite camp as captives. We now reach my struggle.

Moses said to them, "Have you allowed all the women to live? These women here, on Balaam's advice, made the Israelites act treacherously against the LORD in the affair of Peor, so that the plague came among the congregation of the LORD. Now therefore, kill every male among the little ones, and kill every woman who has known a man by sleeping with him." - Numbers 31:15-17

So, here is my struggle. From a strategic standpoint, I guess I can understand why Moses gives the order - prevent boys from growing into men who will seek revenge, the women had not just been innocent bystanders but part of the plot against the Israelites. However, I guess I still find my stomach churned by this order, especially in regards to the children. I find it interesting that this is not one of those situations where "the LORD commanded Moses to say". God is actually silent in this portion of the story. What are we to make of God's silence? God has not shown reluctance to contradict or reprimand Moses for orders in the past. As I read the story, I keep waiting for God to cry out here, kind of like in the story of Abraham and the binding of Isaac. Instead, nothing.

I welcome any comments or thoughts. In the meantime, I guess I will continue to struggle and pray on this one.