I confess to having not given an in-depth study of the claim that God ordered the genocide of the inhabitants of the land of Canaan until forced to face the dilemma head-on. The claim often goes that God decreed that all people be devoted to destruction, viz. death, so that Israel could take possession of the land promised to Abraham. For one, we might understand that fighting men ought to die, but what about those whom we’d label as innocents? The elderly, women, and children? Why is it that they should suffer a harsh fate when they are perceived as innocent according to Christian theology?
If we understand the dilemma as such, it demands a forthright answer. Let’s, first, begin with a passage about the conquest of the land of Canaan.
16 But of the cities of these peoples which the Lord your God gives you as an inheritance, you shall let nothing that breathes remain alive, 17 but you shall utterly destroy them: the Hittite and the Amorite and the Canaanite and the Perizzite and the Hivite and the Jebusite, just as the Lord your God has commanded you, 18 lest they teach you to do according to all their abominations which they have done for their gods, and you sin against the Lord your God. (Deuteronomy 20:16–18 NKJ)
Upon a surface reading, there appears to be a sort of ethnic cleansing ordered. It isn’t that certain individuals are commanded to be destroyed, but entire tribes of peoples. Why? Because they inhabit Israel’s Promised Land and that when they go to take possession of it, they might just as well lead Israel into their idolatry which would displease Israel’s God.
As a person of faith, how we read this command and subsequent following of it determines how we will answer the question. I do not comprehend this command or the conquest as ethnic cleansing or genocide for a few reasons. First, God had promised this land to Abraham, the possessing of it contingent of a specific time upon which the sin of the Amorites would be “complete” (Genesis 15:16). From the timing of God’s promise until the fulfillment of it was to have been more than four hundred years (Genesis 15:13). Therefore, God did not hasten to fulfill this promise but gave ample time for the Amorites, and those in the land, to turn from their ways (cf. Deuteronomy 18:9–12).
Second, when we see earlier occasions of God committing so-called “genocide,” we must ask the reasoning behind this as well. Two other events would be the flood and that of Sodom and Gomorrah. Upon each case of destruction, the wickedness of humanity was so great that it necessitated such a harsh judgment (Genesis 6:5–7). Sodom and Gomorrah lacked just ten righteous people in their cities (Genesis 18:23–33). Nevertheless, the righteous in each of these cases—i.e., Noah and his family and Lot and his family—were spared God’s destruction. This only points to the fact that God keeps the righteous from judgment (2 Peter 2:4–11). Not all of the inhabitants of Canaan were in fact destroyed—e.g., Rahab the Harlot.
However, wherever there is a sin, there is also likely to be victims of sin such as was the case of the outcry against Sodom and Gomorrah (Genesis 18:20–21). We mustn’t think that, as some would have us believe today, that there are victimless sins in all cases of sin. The inhabitants of the land made their children pass through the fire so why doesn’t anyone advocate for the innocent children here who are victimized by their parents’ idolatry? Furthermore, when we understand the literary nature of an epic in the ancient world, such as what Joshua and the Pentateuch are, we understand the usage of poetic language and hyperbole and shan’t be prone to take every single word as literal.
Third, internal to Joshua is the sin of Achan which, as a result of his transgression, brought judgment upon the whole nation (Joshua 7:10–26). Achan’s confession, however, did not appear to be repentance, because he confessed when caught (Joshua 7:17–21). Not only did Achan violate God’s expressed instruction to devote all things to destruction, but he also coveted which led him to exercise a lack of spiritual discernment. A takeaway is that when sin enters among people, if unaddressed, destruction results. The beauty of a community of God (church) is that we are to help one another in weakness and indeed are not to tolerate corruption. Paul said that a little leaven leavens the whole lump, so we too should take care not to permit the leaven to enter among us lest it affects the entire congregation. Because the inhabitants of Canaan lacked such checks and balances, their idolatry became a way of life.
Fourth, other passages from the Bible present a depiction of gradual expulsion versus immediate annihilation, so there’s a decent chance that many of the “innocents” escaped before the actual time of fighting arrived.
27 I will send My fear before you, I will cause confusion among all the people to whom you come, and will make all your enemies turn their backs to you. 28 And I will send hornets before you, which shall drive out the Hivite, the Canaanite, and the Hittite from before you. 29 I will not drive them out from before you in one year, lest the land become desolate and the beasts of the field become too numerous for you. 30 Little by little I will drive them out from before you, until you have increased, and you inherit the land. 31 And I will set your bounds from the Red Sea to the sea, Philistia, and from the desert to the River. For I will deliver the inhabitants of the land into your hand, and you shall drive them out before you. 32 You shall make no covenant with them, nor with their gods. (Exodus 23:27–32)
From this passage, and others (cf. Leviticus 18:24–28; 20:22–23), God gradually but not wholly drove out the inhabitants. He wouldn’t leave the land desolate lest the animals take it over and it became incapable of sustenance or management. Whoever remained, as far as we know, were likely strong and could endure the chastisement of the Lord, but this is only conjecture. A careful reading of Joshua may be in order here to determine this.
Suffice it to say, there are several reasonable explanations from Scripture that diffuse the tension of a generalization of the conquest. These, also, preserve the character and holiness of God. I’m sure much more could be said on the topic—for example, why the descendants of Canaan were cursed for what their father had done (Genesis 9:18–25)—but we’ll leave it here for now.
 The Hebrew phrase “saw the nakedness of his father” in Genesis 9:22 frequently meant “to copulate with.” Since the Canaanites were notorious for sexual perversity (cf. Genesis 34), this may be a viable interpretation. However, no one has entirely solved the puzzle of exactly what Ham did here.