The word genocide gets thrown around a lot when people try to criticize God and the clearing out of the Promised Land. Richard Dawkins particularly likes it, especially when trying to dodge debates with William Lane Craig.
That term fails on a couple of levels, not the least of which is that these people were thoroughly guilty. They had done all sorts of things such as sacrificing their children on super-heated metal images of their gods (see Leviticus 18 for a laundry list of things these charmers had done for 400 years).
I highly recommend this link for an overview of the Canaanite issue: We Don’t Hate Sin. So We Don’t Understand What Happened To The Canaanites. Too many Christians try to apologize for God and rationalize away the meaning of the text. I remember one guy teaching a Bible study who insisted that God didn’t really say that, but the Israelites made it up to rationalize taking over the land. This is far too common.
The question that remains is what do you think of God for commanding such a thing? Does God have a right to do with His creation as He pleases? If you have a problem with the selective judgment of the Canaanites then how do you feel about the almost complete destruction wrought by God of the whole world during the Flood? And how do you feel about the impending destruction of everything at Armageddon?
Too many people made themselves god and the arbiters of what is good and evil, and even those standards are flexible and incoherent.
We need to look to God for what is truly holy. He is the Lord of the universe, and He sets the terms and conditions. His terms of surrender are wildly generous, but you must come to him on his terms, not yours.
P.S. Speaking of God’s holiness, you can currently get a free Kindle version of The Holiness of God by R.C. Sproul! (You don’t have to have a Kindle to read it — you can use the PC Version of the Kindle).