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In Numbers 31:2, God tells Moses and the children of Israel to take vengeance on the Midianites and so they killed all their males. When Moses found that the women made the men of Israel to stumble, he was upset that they were not killed as well (Numbers 31:15). This is one example of many that I came across while reading and did not understand. I know that God says, "Vengeance is Mine" in Deuteronomy 32:35 and that He sent His angel to kill thousands of Assyrians in one night (2 Kings 19:35). My question is why would God command the children of Israel to slaughter others, especially since He could have easily done so Himself? In other cases, I tried to think that it was Moses that allowed the children of Israel to commit these things for the hardness of their hearts like Jesus said about divorce (Matthew 19:8), but in this specific case, God is the one who told them to kill. I know that the Holy Bible says God is even kind to the evil and lets His sun shine on the good as well as the wicked...verses from the Old Testament. I just do not understand why God would specifically tell His people to kill when He commands them "you shall not commit murder" (Exodus 20:13). 
 
Also, I was reading Nehemiah and in 13:25, Nehemiah says that he saw people marrying outside from the children of Israel and "so I contended with them and cursed them, struck some of them and pulled out their hair, and made them swear by God..." Now I know he is a prophet of God, and one of His righteous and elect people. Why would he do this? I do not doubt that it was for a good cause, but I just do not understand how someone representing God could do this when our Lord came down and didn't hide His face from the shame of spitting. Our Lord came and rebuked people but in a firm yet gentle manner. I know that God is more compassionate and loving than it is comprehensible, so when I read things like this, it does not settle well. I have asked about it before but never got an answer that really put me at ease. I know that God is the same and unchanging, from the Old Testament to the New Testament and to the end of ages, so why He did not only allow things like this, but even commanded some in the Old Testament is difficult to understand. 

The children of Israel lived at a time when it was necessary for them, being the only culture that had a real relationship with God, to keep themselves in purity, in every aspect and detail. They had to be governed by strict rules and guidelines. Yet, God was very patient with many nations that oppressed Israel. Nonetheless, He grew tired of the ongoing nonsense of the pagan cultures and their detestable corruption and violence toward His children. God did not want His children to have any share with any polluted environment. They needed to adhere to God's law and principles because they were assured that the Messiah was to come from the lineage of David the prophet, as He promised.

The examples you provide actually help us to perceive that God allows His children to engage in military obligations and operations. It is true that God did not only command us not to kill, but also to not oppress anyone, nor slander anyone's reputation because these forms of harassment are the most commonly used to could kill a person's drive, purpose, and self-esteem. Nehemiah knew how the women were accomplices in many despicable practices in the false faiths at that time. He was disappointed by the mixing of faiths, rather than just cultures. As we learn from Ruth and others, God had always wanted the Gentiles to be amongst His people, but it had to come from them. Many witnessed God's mighty arm in so many miracles and with so much power, and they knew there was no other like Him! God is kind and most compassionate with everyone.