The Amakelites and the Midianites might quarrel with the morality espoused in the Old Testament, had they not all been murdered or sold into slavery and concubuinage on the alleged orders of God.
Re: the Amakelites--
"Now go, attack the Amakelites and totally destroy everything that belongs to them. Do not spare them: put to death men and women, children and infants, cattle and sheep, camel and donkeys." - 1 Sam 15:3
A point of clarification here. Let's put this verse into context (the bold is mine):
1Samuel also said unto Saul, The LORD sent me to anoint thee to be king over his people, over Israel: now therefore hearken thou unto the voice of the words of the LORD. 2Thus saith the LORD of hosts, I remember that which Amalek did to Israel, how he laid wait for him in the way, when he came up from Egypt. 3Now go and smite Amalek, and utterly destroy all that they have, and spare them not; but slay both man and woman, infant and suckling, ox and sheep, camel and ass.
I Sam. 15:1-3
Verse 2 gives us the reason the Lord told Saul to destroy the Amakelites. If you continue on you will read:
9But Saul and the people spared Agag, and the best of the sheep and of the oxen and of the fatlings, and the lambs, and all that was good, and would not utterly destroy them; all that was despised and worthless they utterly destroyed.
So Saul spared the King, and technically they were not all wiped out. Okay, it's a small point, but it's important to keep things straight as much as possible - at least to me.
Just for fun, here is the result of what Saul did:
22 And Samuel said, Hath the LORD as great delight in burnt offerings and sacrifices, as in obeying the voice of the LORD? Behold, to obey is better than sacrifice, and to hearken than the fat of rams. 23 For rebellion is as the sin of witchcraft, and stubbornness is as iniquity and idolatry. Because thou hast rejected the word of the LORD, he hath also rejected thee from being king.
Why is all this even in the Bible? It's there as a testimony and as a example to us. The lesson here, to me is that God detests stubbornness and disobedience (and that means I'm in *big* trouble!).
Re: the Midianites:
"Now therefore kill every male among the little ones, and kill every woman that hath known man by lying with him. But all the women-children, that have not known man by lying with him, keep alive for yourselves." Num 31:17
The Midianites were worshipers of Baal-peor. They joined forces with Balak, the king of Moab, to entice the Israelites to join them in licentious orgies connected with the worship of Baal-peor. (Num. 22:4-7) The Israelites took part in the heathen festivals and orgies, and brought upon themselves a terrible punishment -- a plague that killed more than 24,000 of them. (Num. 25:9)
The destroying of the Midianites was God's punishment upon them for their behavior.
I'm not trying to be inflammatory here. I just have a very difficult time reconciling the notion of a just and merciful God with some sections from the Old Testament, and I'm curious as to how others are able to do so.
Sometimes I just have to remind myself that God sees all and knows all and I don't. I have this finite little mind and can't begin to comprehend the way God does. I simply have to take things on faith and move on with things that I can understand and do things with (such as learning to not be so stubborn).