Why Did God Order Killing?

Our little four year old is very determined to try to keep with his bigger brothers. That often means that he will push himself to run and climb beyond his level of strength and coordination, thus he will often fall and hurt himself. He then comes running to me saying, “Daddy, I have an auwee!”
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When I hear that one of our children has been hurt, my heart aches. My desire is to protect them and to keep them safe. I worry about them falling and getting seriously hurt. I worry about them crossing the street and getting hit by a car. I worry about bad people hurting them.
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As much as we have to worry about here in South Dakota, I am thankful that we do not have the worries that people in other parts of the world face. For example, in the Middle East, fathers have to worry about ISIS capturing their children, torturing, and killing them. I cringe to even write this, but children are actually being decapitated.
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The news reports of the atrocities of the Mexican drug cartels are just as brutal as those of ISIS. I do not bring up these issues to sensationalize violence, but rather to point out the presence of evil in our world.
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Imagine that you were a father or a mother living in the middle east and you had witnessed the terrible deeds of ISIS in your area. Imagine that you were fearful that your family would be the next news report. Now imagine if some soldiers who were opposed to ISIS came on the scene and destroyed the whole ISIS army along with their wives and children. You would likely be quite relieved.
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You could argue that the wives and children should be spared, but imagine that they were fighting right along side the grown men. Image that they were supportive of everything that the men were doing. Imagine that their destruction just saved your family from being the next victim of their slaughter.
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In an ideal world, the women and children would not have to be killed along with the fighting men. In an ideal world, no one would have to be killed in order to stop a murderous rampage.
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We live in a sin cursed world not an ideal world. Many non-Christians have been critical of God because He ordered the absolute destruction of the Amalekites. Deuteronomy 25:17-19 explains why, "Remember what Amalek did to you on the way as you were coming out of Egypt, "how he met you on the way and attacked your rear ranks, all the stragglers at your rear, when you were tired and weary; and he did not fear God. "Therefore it shall be, when the LORD your God has given you rest from your enemies all around, in the land which the LORD your God is giving you to possess as an inheritance, that you will blot out the remembrance of Amalek from under heaven. You shall not forget.” (NKJV)
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The Amalekites were murderers of innocents much like ISIS. As the Israelites were fleeing slavery in Egypt (as Moses was leading them through the wilderness) the Amalekites came and attacked the weakest of the people. God then gave them years to repent, but they continued to be an evil people. God understood that the children would grow up to be just as evil as their parents were, so He ordered them all to be destroyed. This is not an evidence of an evil unloving God, this is evidence of a God of justice who wants to protect the innocent.
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Years later, God actually sent the prophet Jonah (the man swallowed the whale) to the city of Nineveh where many evil people lived, to give them a chance to repent so that God did not have to destroy them. They did repent and were saved. Jonah was actually upset because he thought they should be destroyed. God does not throw around His justice for no reason and even when justice is deserved, He shows mercy.