Thou shall not kill? God says thou shall not kill as one of the Ten Commandments but he actually instructs his chosen people to kill numerous times throughout the Old Testament. Then there is tons of killing, persecution, and even torture performed under the authority of the Catholic Church under the New Testament. Specifically I would like to sight the story of Saul when he is instructed to kill everyone of the Amalekites men, women, and children. Saul failed to do so and he was actually punished for it and would eventually lose his annionted kingship. So in short my question is:

Why does God condone or order so much killing when it is against the Commandments?
Exodus 20:13 (NIV) “You shall not murder.
  
  Exodus 20:13 (KJV) Thou shalt not kill.


The meaning* of the Hebrew word for "kill/murder" used in this verse has a wide range of meanings as explained in  this article. The act of killing in a warfare is not what this 6th commandment means.

The commands for the killings in the Old Testament had proper reasons. 


  Deuteronomy 20:16-18 (NIV) However, in the cities of the nations the
  Lord your God is giving you as an inheritance, do not leave alive
  anything that breathes. Completely destroy them—the Hittites,
  Amorites, Canaanites, Perizzites, Hivites and Jebusites—as the Lord
  your God has commanded you. Otherwise, they will teach you to follow
  all the detestable things they do in worshiping their gods, and you
  will sin against the Lord your God.



To annihilate all the inhabitants of Canaan:  God promised the land of Canaan to the people of Israel. It was necessary to annihilate all the inhabitants of Canaan before they could settle there. It is logical that no one will allow a foreigner to occupy his land. Israelites had to fight their way into Canaan in order to rule and possess it. Once the whole promised land was occupied, God never commanded them to extend their territory by attacking their neighboring countries. The whole Canaan was taken under the rule of David, and after him God never commanded them to extend their territory.
To get rid of Idolaters: God did not want the Israelite to mingle with the idolaters in Canaan less they also become like them. God also did allow them to marry idolaters. It was the command of God to annihilate all idol worshipers in Canaan but the Israelites failed to do it which resulted in idolatry in Israel. This idolatry caused the destruction of Israel under Assyria and Judah under Babylon. 


Regarding the killings and tortures done by the Catholic Church, it had more to do with politics and ignorance, rather than the commands in the Bible nor from God.



* As Caleb commented, the meaning of the word "kill" could mean "murder" at the time when KJV was written.