Jamieson, Fausset and Brown on Numbers 31:14-18

14-18. And Moses was wroth with the officers of the host--The displeasure of the great leader, though it appears the ebullition of a fierce and sanguinary temper, arose in reality from a pious and enlightened regard to the best interests of Israel. No order had been given for the slaughter of the women, and in ancient war they were commonly reserved for slaves. By their antecedent conduct, however, the Midianitish women had forfeited all claims to mild or merciful treatment; and the sacred character, the avowed object of the war (Nu 31:2, 3), made their slaughter necessary without any special order. But why "kill every male among the little ones"? It was designed to be a war of extermination, such as God Himself had ordered against the people of Canaan, whom the Midianites equalled in the enormity of their wickedness.