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Even though God said in the Mosaic that thou shall not kill but in the book of Numbers 15:32-36 He ordered Moses to make all the congregation to stone outside the camp. This situation does not break that law because God himself is the Author of that law. He is the maker of humankind and at that time the of Israel were under law but not Grace. Even the Bible says in the book 1 Sam 2:30-31(NIV):
30 "Therefore the Lord, the God of Israel, declares: 'I promised that your house and your father's house would minister before me forever.' But now the Lord declares: 'Far be it from me! Those who honor me I will honor, but those who despise me will be disdained".
This means that was what He want to do and He made and it doesn't go against any of His law given to his people. He is All-Knowing and all wisdom belong to him.