I think the easy first step to misunderstanding God's motives is to misunderstand and/or misconstrue his message. In spite of what many have claimed, I don't believe the Bible ever has condoned rape.

http://www.gotquestions.org/Bible-rape.html

Similarly, slavery is not exactly as black and white as we interpret it today.

http://www.gotquestions.org/Bible-slavery.html

Finally, even genocide may have had its reasons.

http://www.gotquestions.org/Old-Testament-violence.html

I don't agree with every answer this site gives, and as you know, Mormons interpret some of the Bible differently anyway, but it at least gives an idea. But the point is that the God of the Old Testament is often merciful, not just vindictive. Remember how the Bible teaches of God's compassion towards the Ninevites when sending Jonah to teach them.

Also bear in mind the near-consequences of having not followed through on an order for killing an entire people: in the story of Esther, Haman, a descendant of the not-quite-extinct Amalekites, nearly had the Jews in Persian captivity destroyed.

Finally, at least one ancient scholar even argued that destruction was initially an offer of peace and a commandment to accept God's laws, and if rejected, then came destruction.

Now I'll be honest, these answers don't completely satisfy me, but it at least helps me see that perhaps there is a bigger view that escapes me at the present.