The events of the Book of Joshua are troubling to deal with, yes.
Actually I once heard a sermon that was more of an interview between the pastor and a prominent Old Testament scholar who teaches at a seminary here, with at topic of basically "what violent and unsettling stories in the Bible really mean" with that book being the primary focus. The way she explained it is that it was more of a war story and allegorical to the ancient Israelites, and that archaeological evidence does not show anything for Jericho's walls crumbling. However there is some evidence that there was a group of slaves that may have escaped from the Canaanites and joined in with ancient Israel, and she later compared it to the Battle Hymn of the Republic and how it was used by slaves during the Civil War and their war anthems and all that. Interesting take.The divine liberation/human war theme is how I've always been most comfortable dealing with that part of the Bible too.
The worst thing about Hitchens was his collocation of political and cultural views, some of which were related to his atheism, some of which weren't.