Actually most Christians, rightly, have a hard time reconciling these things.
I know I do.
There are a few books that have been written on the subject, like the one by Paul Copan.
The issue is, however, the fact ( accoring to the writers) that God commanded this.
The first part that mustbe addressed is was it genocide or "capital punishment"?
I think that there are some that would agree that a people that were shown to be horrific and cruel, practiced infant and child sacrifices and such, would be deserving of "capital punishment", I mean, I am sure that if we look back in history most of us will find at least one group of people that we think God should have "take care" of.
WHat we are doing is trying to justify what God ordered ( if He ordered it), to see if there was some reason that would justify "capital punishment".
The next step is to confirm what really did happen, to seperate the actual acts from the written "hyperbole".