I have a friend who's an atheist. He took a class on the history of genocide and started thinking about the Bible stories about the Israelites invading Canaan. God punished them when they didn't practice total war. My friend was worried that there was something insidious about Christianity that was leading to violence, and the Christian fundamentalist support for the war in Iraq troubled him.
In Sunday school, sometimes we'd get up and march around the room seven times to reenact Joshua and the battle of Jericho. Maybe we'd knock down some blocks or something. Curiously, we didn't then hit baby dolls with plastic swords and set the carpet on fire as part of this play. Joshua and the battle of Jericho isn't a good children's story; if it were made into a movie, no good Christian parent would let their child watch it.
When I was a believing Christian, I had to come up with confusing defenses, reconciliations of barbarism with the notion of a loving God. The conservative way of dealing with stories like this is to do systematic theology to figure out that God is just and sometimes that justice means destroying entire ethnicities, unpleasant as that may be. The liberal way of dealing with stories like this is to question whether they're really stories about God, or mere byproducts of a racist violent society. As a Christian agnostic, I don't need to deal with the stories, I'm under no obligation to be consistent.