Justin Taylor has posted a nice response to the question, "How could God command Genocide in the Old Testament?" In sum, Taylor suggests seven considerations.
1. As the maker of all things and the ruler of all people, God has absolute rights of ownership over all people and places.
2. God is not only the ultimate maker, ruler, and owner, but he is just and righteous in all that he does.
3. All of us deserve God’s justice; none of us deserve God’s mercy.
4. The Canaanites were enemies of God who deserved to be punished.
5. God’s actions were not an example of ethnic cleansing.
6. Why was it necessary to remove the Canaanites from the land?
7. The destruction of the Canaanites is a picture of the final judgment.
I wrote on this topic about a year ago. Here is my discussion.
The extermination of the Canaanites
The complete extermination of the Canaanites evidenced periodically in the Book of Joshua has often troubled interpreters. Furthermore, for some Christian interpreters there is great difficulty in resolving the utter destruction of the Canaanites commanded in Joshua with the teachings of Christ and the gospel. What follows is a very brief reflection on some of the issues that one should take into consideration in working towards a solution.
First, it must be remembered that the extermination of the Canaanites is part of a broader concept related to God’s justice and wrath. That is, God judges sin and metes out the resulting punishment. In the process of punishing sinful people God has the prerogative to use a variety of means, including people to carry out His judgment. Thus the extermination of the Canaanites must be viewed as an extension of God’s sovereignty.
Second, the extermination of the Canaanites must also be viewed within the broader context of YHWH (or Holy) war. The sheer magnitude of the topic is beyond the scope of this argument, however, a few points might prove helpful. By YHWH war we mean a war that YHWH initiates, facilitates, and participates for the fulfillment of His covenantal promises and purposes. Thus, the extermination of the Canaanites in Joshua is not motivated by material greed or by racial or ethnic hatred. Rather, the motivation is tied intimately to the covenantal promises. For
Third, and related to the second point, is the fact that mere displacement is insufficient. The extermination of the Canaanites is necessary for at least three reasons. First, the Canaanites must be removed for prophylactic reasons. That is,
Finally, it should be noted that the extermination of the Canaanites was a limited event. The contention that the Old Testament contains many such events is simply not true. As Christopher Wright notes, “The conquest narratives describe one particular period of
While these observations do not resolve all the ethical and theological difficulties associated with this issue, and while modern sensibilities and geo-political realities tug at the interpreter, for this writer the above provides a necessary and sufficient context for moving towards a resolution.
 God can also use nature (flood, famine, locust invasions, plagues, etc.), angels, or even a person’s own disposition or personality (the hardening of pharaoh’s heart for example).
 For discussions concerning the designation YHWH war see Gwilym H. Jones, “‘Holy War’ or ‘Yahweh War’?,” Vetus Testamentum 25 (1965): 654–8; Rudolph Smend, Yahweh War and Tribal Confederation, trans. Max Grey Rogers (New York: Abingdon, 1970) 36–7; P. U. Lilley, “Understanding the „erem,” Tyndale Bulletin 44 (1993): 173; Eugene Merrill, “The Case for Moderate Discontinuity,” in Show Them No Mercy, ed.
 The classic study of holy war is still Gerhard von Rad’s work entitled Holy War in Ancient Israel, ed. And trans. Marva J. Dawn (Grand Rapids: Eerdmans, 1991).
 Gleason L. Archer, Jr., A Survey of Old Testament Introduction, Updated and Revised ed. (Chicago: Moody, 1994), 273.
 Christopher J. H. Wright, Old Testament Ethics for the People of God (