Why would God order the destruction of men, women, and children?

An atheist friend of mine poises this question:  Why would God order the destruction of men, women, and children?  And cited the following verse to back up his question, "Thus says the Lord of hosts, ‘I will punish Amalek for what he did to Israel, how he set himself against him on the way while he was coming up from Egypt. 3 ‘Now go and strike Amalek and utterly destroy all that he has, and do not spare him; but put to death both man and woman, child and infant, ox and sheep, camel and donkey,” (1 Samuel 15:2-3).

There are two way at looking at this story Christopher The first, most likely the way you interrupt it, and that is it is a story told to justify the Israelites killing any who would resist, remember God told then the same thing at the battle of Jericho, just as Temujin used to tell the cities he was sieging, “Join me or die” on his way to becoming Genghis Khan.  Temujin keeping his promise to each and every city he took lead to many, many more who would not put up a fight and instead joined him and increased his army.

The second is to believe, as I do, that God did order the destruction of men, women, and children in this battle just as he did when He flooded the world, yes I believe that actually happened, and 10th Plagues on Egypt.  But your question is why He did it, not if I believe He did it.  To believe that God flooded the world requires one to believe that God’s scrip does not always run as God wants it to run.  This is tangential to the discussion on predestination and free will but I will not digress.

I believe that God has had a plan from creation to make man first mortal through Adam, and then immortal through Jesus.  God chose Israel to bring this plan into fruition, to discuss that plan is beyond the room or time we have here.  However the Amalekites were the nomads who attacked the Hebrews at Rephidim, Exodus 17:8-10, in the desert of Sinai during their exodus from Egypt: "smiting the hindmost, all that were feeble behind,", and in Numbers 14:43-45, “For the Amalekites and the Canaanites [are] there before you, and ye shall fall by the sword: because ye are turned away from the LORD, therefore the LORD will not be with you.  But they presumed to go up unto the hill top: nevertheless the ark of the covenant of the LORD, and Moses, departed not out of the camp Then the Amalekites came down, and the Canaanites, which dwelt in that hill, and smote them, and discomfited them, [even] unto Hormah.

This was what God was referring to when He said, “I will punish Amalek for what he did to Israel”, and I take it the bitch is that he would not only order the destruction of the men, but both man and woman, child and infant, ox and sheep, camel and donkey?  Remember Num 14:18, “The LORD [is] longsuffering, and of great mercy, forgiving iniquity and transgression, and by no means clearing [the guilty], visiting the iniquity of the fathers upon the children unto the third and fourth generation”?  You may not agree with God, but God is God, and true to His word.  He is the Potter and we are the clay.

Rom 9:15-23, “For he saith to Moses, I will have mercy on whom I will have mercy, and I will have compassion on whom I will have compassion.  So then [it is] not of him that willeth, nor of him that runneth, but of God that sheweth mercy. For the scripture saith unto Pharaoh, Even for this same purpose have I raised thee up, that I might shew my power in thee, and that my name might be declared throughout all the earth. Therefore hath he mercy on whom he will [have mercy], and whom he will he hardeneth. Thou wilt say then unto me, Why doth he yet find fault? For who hath resisted his will? Nay but, O man, who art thou that repliest against God? Shall the thing formed say to him that formed [it], Why hast thou made me thus? Hath not the potter power over the clay, of the same lump to make one vessel unto honour, and another unto dishonour?  [What] if God, willing to shew [his] wrath, and to make his power known, endured with much longsuffering the vessels of wrath fitted to destruction: And that he might make known the riches of his glory on the vessels of mercy, which he had afore prepared unto glory,” 

Amalek was without a doubt a longersuffered vessels of wrath which God had fitted to destruction to make his power known.  There it is, believe it or not God’s will will be done.   But Saul did not do it, even so God's will was done.

But Saul and the people spared Agag and the best of the sheep, the oxen, the fatlings, the lambs, and all that was good, and were not willing to destroy them utterly; but everything despised and worthless, that they utterly destroyed. Then the word of the Lord came to Samuel, saying, "I regret that I have made Saul king, for he has turned back from following Me, and has not carried out My commands." And Samuel was distressed and cried out to the Lord all night (1 Sam. 15:9-11).  Leading thus to David's rise.