I went back to look over what you wrote again, I realized mostly you had posted Scripture, with some commentary, so I looked more closely. I think that God's rules for man don't neccesarily match what God does of Himself. We are told to give to others, for instance, but God does not always give. Sometimes people starve to death. If I do it, it is wrong to not feed them if I can, but God allows them to starve. His ways are not our ways.If you want to hear my answer (which is not that protracted) you will need to read it.
And I think, for instance, when God strikes someone dead - think Elijah on a hilltop, "If I be a man of God . . .", God sent that fire that killed the captain and his 50. And it wasn't wrong for Him to do that. When the disciples asked if they should call fire down, Jesus told them, You don't know of what spirit you are.
There is a time and a place, and it's not up to you or I to choose, but for God. And God did in fact choose for these things to be done. The captain and his 50. The slaughter of Amelek. The slaughter of the priests of Ba'al. And even David his 10,000's. God's command was to destroy the inhabitants of the land, to possess it for themselves.
I don't see assumptions, and I don't see contradictions, but that's just me.
Much love!