1) It's an Old Testament problem, which the New Testament puts right.
2) The Israelites thought it was what God commanded, but they were wrong.
3) It is all meant as an allegory of spiritual warfare.
Views 1 and 2 are really just flip sides of the same coin but he addresses each individually. He says with reference to the second view:
"But the main problem with this view is that everywhere in the Bible the conquest is never explained away as a colossal mistake; on the contrary, it is anticipated, commanded, achieved, and remembered as something that accomplished God's will." (emphasis his)and
"You simply can't surgically remove the conquest alone from the great sweep of Bible history, saying that it was merely the bloody actions of deluded warriors, while leaving all the rest of the story intact within the sovereign will of God. At least, you can't if you treat the Bible seriously as a whole." (p. 82-83)The following chapter provides "three frameworks" in which to understand the conquest. The God I Don't Understand is a good book for those struggling with some of the tough questions of faith.
It is a hardcover from Zondervan with 224 pages and sells for $19.99.