God chose a people. The people needed a land. The land was taken from the people who owned it, who were under judgment. That is as far as it went. There was no expansion of territory, of genocide near and far throughout the middle east. People died. Yes. At a time in history, for a purpose. Then it ceased. I'm afraid I cannot explain it better than that. I believe God has rights over His creation. He has the right to wipe out everyone, but He didn't and he doesn't.

I think that with the sparse information we're given, it would be extremely presumptuous to try to judge God on such matters. The truth is that we do not know exactly why some things happened in many cases, but we have learned by experience that God loves us and is a God of love. He is passionate about his children and will do what is best for them. Christ suffered cruelly and laid down his life for us. What more evidence of love do we desire from him? One of my favorite case studies on God's having wiped out a group of people occurs in the Book of Mormon. God wiped out the city of Ammonihah, which was a wicked city. The righteous were persecuted and the wicked governed. I think it is very rarely apprehended why God destroyed the city. In this case, the lawyers and judges of the city were studying how they might overthrow the liberty which their form of government guaranteed its citizens (see: Alma 8:16-17 http://scriptures.lds.org/en/alma/8/16-17#16). God sent a prophet to call the people to repentance, the wicked people expelled or killed the righteous, and, there being no righteous left among them, they were destroyed. A good opposite case in point is Ninevah. I don't think we are told very explicitly what Ninevah was doing that God felt it expedient that they might be destroyed, but he sent in a prophet (Jonah) and they repented. Destruction was averted. I think these are slightly different models than the one being discussed, but nonetheless they are instructive in God's judgment and the mercy which he accords us.

Perhaps you mean reconcile. I suggest you just regard it as another clear indication of interference with scriptures and ignore it. God does not promote death and destruction. If we look at the wisdom of creation we see the things He has put in place are pointing in the opposite direction, towards sustaining and reproducing life, not destroying it. Just look at one example, closest to us, see how the rise and fall of strength, beauty and cross gender attraction in a human being’s life coincides with the rise and fall in their ability to reproduce. The value and sanctity of life is captured in HQ 5:32 which says “if any one slew one person - unless it be for murder or for spreading mischief in the land - it would be as if he slew the whole of mankind and if any one saved one life, it would be as if he saved the whole of mankind.” As for violence as a way of getting people to believe, the Islamic principle here rules out not only killing but any form of coercion, which may even include bribery. This principle is stated in HQ 2:256 which says “Let there be NO COMPULSION in religion: good guidance stands out clear from error: whoever rejects evil and believes in God hath grasped the most trustworthy hand-hold that never breaks. And God heareth and knoweth all things” Destruction is man’s evil as HQ 5:32 goes on to say “Then although there came to them Our messengers with clear signs, yet, even after that, many of them continued to commit excesses in the land” Let alone humans even the destruction of crops and animals is forbidden by Yahweh as indicated in HQ 2:205 describing a wicked person “And when he turneth away (from thee) his effort in the land is to make mischief therein and to destroy the crops and the cattle; and God loveth not mischief.” Translation of the HQ by Mr Pickthall and others.