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There are at least three responses to the assertion that God was wrong to command the destruction of entire cities, including women and children:
Some argue that God was wrong to command the destruction of entire cities, including women and children. Here are several relevant passages:
Numbers 31:15-18- 15 Moses said to them, “Have you let all the women live? 16 Behold, these, on Balaam's advice, caused the people of Israel to act treacherously against the Lord in the incident of Peor, and so the plague came among the congregation of the Lord. 17 Now therefore, kill every male among the little ones, and kill every woman who has known man by lying with him. 18 But all the young girls who have not known man by lying with him keep alive for yourselves.
Deuteronomy 2:33-34- 33 And the Lord our God gave him over to us, and we defeated him and his sons and all his people. 34 And we captured all his cities at that time and devoted to destruction every city, men, women, and children. We left no survivors.
Judges 21:10- So the congregation sent 12,000 of their bravest men there and commanded them, “Go and strike the inhabitants of Jabesh-gilead with the edge of the sword; also the women and the little ones.
1 Samuel 15:2-3- 2 Thus says the Lord of hosts, "I have noted what Amalek did to Israel in opposing them on the way when they came up out of Egypt. 3 Now go and strike Amalek and devote to destruction all that they have. Do not spare them, but kill both man and woman, child and infant, ox and sheep, camel and donkey."
There are at least three different answers we can provide for those who claim that God was wrong in ordering the destruction of entire cities, including women and children.
The Bible clearly teaches that "None is righteous, no, not one" (Romans 3:10
This means that every human being deserves punishment, death, and hell, including women and children, who are also guilty of sin before God. Although women and children sometimes appear to be innocent by human standards, they are simply guilty of sin and deserving of God's wrath from God's perspective.
Therefore, when God commanded the death of everyone in an entire city, that death is what those people ultimately deserved in the first place. God's command simply resulted in an earlier death and punishment for those people.
Throughout history, Israel struggled much with temptation and idolatry from other nations, which oftentimes led Israel into grievous sin (for which God oftentimes punished them with death).
When God commanded the destruction of entire cities, one of the purposes was to keep Israel, His chosen people, pure from temptation and idolatry. If Israel had left these cities intact, it would have been tempted and drawn away from purity in worship and serving God.
When a non-Christian argues that God is wrong because of something He did or commanded, we should ask this person, "By what objective moral standard do you judge God's actions to be wrong?"
Those with secular worldviews do not have such an objective moral standard. They can really only steal the biblical worldview's objective moral standard, which invalidates their argument in the first place.