Why does God condone killing in the Old Testament?

Many people feel like God is being contradictory in the Old Testament by stating that people should not kill, but then telling the Israelites to conduct mass killings of certain people groups.  However, there is a difference between what is going on between the two.  When God says, thou shalt not kill (Exodus 20:13) He is talking about blatant murder, just killing for the sake of killing.  However, when God told Israel to kill those groups of people He did so through judgment of those people.  He had given them all plenty of chances to turn away from their sins, yet they refused (some He gave upwards of 400 years; Genesis 15:13-16).  Also God does allow the Israelites to exercise the death penalty many times over for various kinds of murder and extreme offensive crimes (Exodus 21).  So while God does not want us to just go around and kill people, He does use death as punishment in judgment.