I think when we speak about events that occur in the Hebrew Bible that others seem to think are "troubling," we need to ask what these same people think about God and more current troubling events. How one answers the following questions may help understand how he approaches these passages in Scripture, as it indicates his theology of who God is and how He is related to events in the world.
So I'm going to attempt to ask this question, which I realize is likely a dangerous one, concerning God and the holocaust. One could ask the same about tsunamis, earthquakes, shootings, wars, etc.
In relation to the holocaust was God:
A. All-powerful and evil and orchestrated the holocaust because He wanted humans to suffer.
B. All-powerful and good and orchestrated the holocaust because He wanted to accomplish a greater temporal or eternal good.
C. All-powerful, did not orchestrate the holocaust, but chose not to stop it due to His apathy toward those dying.
D. All-powerful and good, did not orchestrate it, but chose to go ahead and use it later for some good (making the lemons that humans gave Him into lemonade), so He chose to let it continue until men put a stop to it.
E. Not all powerful, so although He did not orchestrate it, and hated it, He had no ability to stop it. Hence, He wept helplessly at this event along with everyone else who was helpless.
F. All-powerful and good, but didn't know the holocaust was going on because He was on vacation when it happened.
Obviously, we could put an "G" here for the atheist who believed that God was not existent, so it took place apart from His interaction, but my point here is to draw out one's view of God and how He works in the world.
Christian answers throughout history have waxed between B and D, but when we look to the Bible, option "D" is not what we find. Instead, we see option "B" all over the place, which makes more sense with God's abilities and nature.
When I say "orchestrates," of course, I don't mean He wants evil to be performed by anyone, but only that He directs evil and suffering, which is already in the world to destroy, to accomplish a greater goal that saves people in some way rather than destroys them. But this means that some people are, in fact, destroyed that others might be saved and live. The holocaust was surely a great evil performed on the part of human beings, but it brought about a great many goods in terms of how we think about violence toward other people purely because of their ethnicity. It also brought about the restoration of the Jews to their own homeland (although some don't consider this a good). It also brought about a lot of sympathy and second thoughts about how the Jews should be treated while they live in other nations. Those are just some of the good things we can see. There may be countless other goods that have come about from this event that, without which, may have never occurred. In essence, it may be that a future extermination of the Jewish people that would have been completely successful was thwarted by the occurrence of the holocaust. Who knows?
The point is that if God orchestrates these things by necessity of His nature and goals, then God orchestrates tsunamis, wars, and other destructive events for His ultimately good purposes. What that means is that when we approach whether God orchestrated the Canaanite conquests, biblical tribal wars, etc., the answer must be, Yes. What that means even further is that the biblical picture of God and His orchestrating those events verbally is closer to reality than assuming that ancient people just made it up to justify their evils.
Now, of course, one would have to argue that what these humans did was not evil on other grounds (namely, that God verbally and directly ordered these events as opposed to merely directing evil to its own destruction through them). The Nazis are guilty of horrendous crimes for which they will be judged by God. They were not ordered by God to do them. Hence, a direction of evil is not the same as ordering a good that others may view as evil. There is nothing evil about just war that defends and preserves human lives against destroyers. There is nothing evil about a civil war that is waged to stop a racist and abusive slavery. Hence, there is nothing evil about entering into a dark event and even directing it there in order to secure a greater good. The question is whether God can be divorced from any event at all, and if He cannot be, how He is linked to it.