As I was reading The Bible Jesus Read today I realized something… Now, let me preface this by saying I've always assumed God had a perfectly just and reasonable cause for telling the Israelites to wipe out an entire culture. It's never hurt my faith, I've just never cared to put time into this one. But to hit the ground running when the time comes for me to look into this, I realized that God had every right and was perfectly justified in asking the Israelites to annihilate the Amalekites. God is a God of personal relationships, and not one of the Amalekites had a personal relationship with God, or ever would. In fact, it could quite rightly be said that they were a waste of flesh. All they cared about were themselves and pleasure. God gave them life, but they wasted it, and their continued existence would cause the corruption of people that God did have a personal relationship with.
Oh, that's why God killed the Amalekites!