It is a profound question. Here is my answer.
On one hand, the Bible clearly states God ordered the genocide.
Jericho and everything in it must be completely destroyed as an offering to the LORD. Only Rahab the prostitute and the others in her house will be spared, for she protected our spies. Joshua 6:17 NLT
And the LORD said unto Joshua, Fear not, neither be thou dismayed: take all the people of war with thee, and arise, go up to Ai: see, I have given into thy hand the king of Ai, and his people, and his city, and his land: And thou shalt do to Ai and her king as thou didst unto Jericho and her king: only the spoil thereof, and the cattle thereof, shall ye take for a prey unto yourselves: lay thee an ambush for the city behind it. Joshua 8:1-2 KJV
A “plain reading” of these Bible passages leaves us with a simple answer to the question, “Did God order the genocidal acts of Israel?” Yes. But, I counter, there are a number of other passages which Adventists (and many other Christians) “explain” in ways that avoid the plain meaning.
God hardened Pharoah's heart. Exodus 9:12
And again the anger of the LORD was kindled against Israel, and he moved David against them to say, Go, number Israel and Judah. 2 Samuel 24:1
Now therefore, behold, the LORD hath put a lying spirit in the mouth of all these thy prophets, and the LORD hath spoken evil concerning thee. 1 Kings 22:23
If we take the plain reading of the Bible in the above texts, God is an active participant in evil. So Advnetists (and others) have reinterpreted these texts in various ways to avoid saying that God actually did the very thing the Bible says God did. Since these statements are in the same historical context as the passages that say God ordered the genocide, I see no reason not to employ the same methods of interpretation. Which means we acknowledge the text says “God did it” or “God said it” but actually God did not do it or say it.
Some argue that moral revulsion to genocide is a purely modern thing, that if we had been back there in history, we would have had no problem with God ordering genocide. But the Bible itself includes strong protests against the notion of divinely-ordered or divinely-caused genocide. When God announced genocide against Sodom, Abraham protested such an act would be wrong for someone who had the title “Judge of All the Earth.” God bent to Abraham's protest and agreed the presence of even ten good people will be sufficient to prevent the divine blast. When the angels could not find ten good people, they evacuated the four “good” people, thus validating Abraham's fundamental instinct of objection to the slaughter of the innocent and guilty together—which is one of the inescapable effects of genocide.
When God explicitly ordered Moses to step aside and allow God to perpetrate genocide on Israel in the aftermath of the Golden Calf incident, Mosed refuses to step aside. And God backed down. Moses was right and God was wrong. Or God as portrayed in the plain reading of the story. Usually this story is reinterpreted this way: God did not literally intend to annihilate Israel. Instead, God's words to Moses dramatized the evil the people had done and prepared the way for Moses to act as a savior, thus prefiguring the work of Jesus. I like this interpretation, but we must acknowledge it is a departure from the plain reading of the text. According to the text, God announces genocide and Moses adamantly protests and blocks the divine plan.
When we consider the genocide against the Canaanites, we note the divine pronouncement of doom was so well known the Canaanite peoples themselves knew of the decree. One group of Canaanites, the Gibeonites, tricked the Israelites into signing a mutual non-aggression treaty because of their familiarity with the divine order of genocide. Even though the divine decree was utterly clear, Joshua faced down his entire army when they insisted on obeying God and wiping out the Gibeonites. Joshua deliberately, forcefully opposed the divine verdict of doom. Curiously, when decades later, King Saul decided to do what Joshua had refused to do, God sided not with King Saul but with the Gibeonites. (See Joshua 9 and 10 and 2 Samuel 21.)
So when we say that genocide is immoral and unworthy of God, we are standing with Abraham, Moses and Joshua. Our opposition to genocide is not a modern invention. It is rooted in the most profound human sense of justice and righteousness.
Given the examples of Abraham, Moses, and Joshua, our own rejection of the idea that God really, truly ordered the annihilation of entire populations is on solid biblical grounds. We are insisting that the entirety of the Bible be brought into the discussion.
I argue that the opposition of these men to the command of God is the ancient writers' way of challenging the deeply-embedded conviction of their people that God condoned genocide. It seems to me there are at least a couple of plausible interpretations of the texts: Either God ordered genocide, then changed his mind when confronted by people more merciful than he was or God never actually intended to the genocide in the first place.
I prefer the second interpretation. I don't think God ever commanded genocide against the Canaanites.
Some people, explaining why the Canaanites needed to be annihilated, say that it was because the Canaanites were so debauched that they had to be eradicated to prevent the moral collapse of all humanity. There are problems with this idea.
First, and most important, when we come to the writings of the prophets we find them repeatedly challenging the notion that the Jewish people were superior to their neighbors.
As surely as I live, says the Sovereign LORD, Sodom and her daughters were never as wicked as you and your daughters. Sodom's sins were pride, gluttony, and laziness, while the poor and needy suffered outside her door. She was proud and committed detestable sins, so I wiped her out, as you have seen. "Even Samaria did not commit half your sins. You have done far more detestable things than your sisters ever did. They seem righteous compared to you. Shame on you! Your sins are so terrible that you make your sisters seem righteous, even virtuous. "But someday I will restore the fortunes of Sodom and Samaria, and I will restore you, too. Then you will be truly ashamed of everything you have done, for your sins make them feel good in comparison. Yes, your sisters, Sodom and Samaria, and all their people will be restored, and at that time you also will be restored. Ezekiel 16
A second point I would make is that if the purpose of the genocide was to eradicate the risk of spiritual contamination of Israel, that purpose utterly failed. The genocide was actually rather very limited. Only a few cities were annihilated but large swaths of the land were left in the control of the Canaanites. For example, Jerusalem remained in Canaanite hands until the time of David. (See the book of Joshua for details.) And through their early years, Israel was a raunchy, violent society. (See the book of Judges.)
I take as my principle text for understanding God, the three stories in Luke 15. In this chapter there is no hint of punishment or damnation. Instead, the first two stories end with all gathered in, one hundred sheep in the fold, ten coins back on the necklace. The last story ends with the Father's declaration to the older son, the one who is most persistently alienated from the generous heart of the Father: Son, all that I have is yours. Not will be, could be, or might be. But is.
This Father never ordered or condoned genocide. He never will.