This is a good, hard question. The way we answer it will both reflect and inform our understanding of justice and mercy.

The question is about what happens in the book of Joshua when God commands Israel to slaughter the Canaanites in order to occupy the Promised Land. It was a bloody war of total destruction where God used his people to execute his moral judgment against his wicked enemies. In moving toward an answer it will be helpful to think carefully about the building blocks of a Christian worldview related to God’s justice and mercy.

1. As the maker of all things and the ruler of all people, God has absolute rights of ownership over all people and places.

“In the beginning, God created the heavens and the earth” (Gen. 1:1) “and the sea and all that is in them” (Act 14:15). This means that “The earth is the LORD’s and the fullness thereof, the world and those who dwell therein” (Ps. 24:1). As God says, “All the earth is mine” (Ex. 19:5) and “every beast of the forest is mine” (Ps. 50:10). God’s ownership of all means that he is also free to do as he wishes over all things. “Our God is in the heavens; he does all that he pleases” (Ps. 115:3). Within this free sovereignty God “determined allotted periods and the boundaries of [each nation’s] dwelling place” (Acts 17:26). God has Creator rights, and no one can say to him, “What are you doing?” (Job 9:12).

2. God is not only the ultimate maker, ruler, and owner, but he is just and righteous in all that he does.

Abraham asks God the same question that we are asking, “Shall not the Judge of all the earth do what is just?” (Gen. 18:25). The implied answer is, “By all means!” This is the flip side of Paul’s question in Romans 9:14: “Is there injustice on God’s part?” Paul’s answer: “By no means!” Moses will later proclaim, “The Rock, his work is perfect, for all his ways are justice. A God of faithfulness and without iniquity, just and upright is he” (Deut. 32:4).

It is commonplace in our culture to ask whether this or that was fair or just for God to do. But if you stop to think about it, the question itself is actually illegitimate. Merely asking it presupposes that we are the judge; we will put “God in the dock” and examine him; God must conform to our sense of fairness and rightness and justice—if God passes the test, well and good, but if he doesn’t, we’ll be upset and become the accuser. Perish the thought. As Deut. 32:4 says, “all God’s ways are justice”—by definition. If God does it, it is just. To think otherwise is the ultimate act of arrogance, putting your own mind and opinions and conceptions as the ultimate standard of the universe.

This does not, however, preclude humble questioning and seeking in order to gain greater understanding. While it is ultimately illegitimate to ask if God’s ways are just in securing the Promised Land, it is perfectly appropriate and edifying to seek understanding on how God’s ways are just—whether in commissioning the destruction of the Canaanites or in any other action. This is the task of theology—seeing how various aspects of God’s truth and revelation cohere.

3. All of us deserve God’s justice; none of us deserve God’s mercy.

As noted above, God is absolutely just in all that he does. The only thing that any of us deserve from God is his justice. We have broken his law, rebelling against him and his ways, and divine justice demands that we receive divine punishment in proportion to our traitorous, treasonous rebellion. It is fully within God’s rights to give mercy, but he need not give it to all—or to any. It is also helpful to note that in biblical history, an act of judgment on one is often an act of mercy for another (e.g., the flood was judgment on the world but a means of saving Noah; the plagues were judgment on the Pharaoh but a means of liberating Israel). Likewise, the destruction of the Canaanites was an act of mercy for Israel.

4. The Canaanites were enemies of God who deserved to be punished.

“All have sinned and fall short of the glory of God”—“None is righteous, no, not one”—and “the wages of sin is death” (Rom. 3:23; 3:10; 6:23). Therefore if God destroyed Adam and Eve after the fall he would have been entirely just. When he wiped out over 99.99% of the human race during the time of Noah, he was being just.

Sometimes we can mistakenly think that God just wanted to give his people land and kicked out the innocent people who were already there. But in reality, the Canaanites were full of iniquity and wickedness, and God speaks of the land vomiting them out for this reason (cf. Gen. 15:6; Lev. 18:24-30; Deut. 9:5). All of this is consistent with the fact that God “avenges the blood of his children and takes vengeance on his adversaries. He repays those who hate him and cleanses his people’s land” (Deut. 32:43).

It’s also important to note Deut. 9:5, which says that Israel’s possession of the land and the Canaanites’ being kicked out would not be due to Israel’s righteousness, but would rather be on account of the Canaanites’ wickedness. God very pointedly tells Israel that if they do not follow the Lord and his law, then they will suffer the same fate as the nations being vomited out of their land (cf. Lev. 18:28; Deut. 28:25-68; cf. also Ex. 22:20; Josh. 7:11-12; Mal. 4:6). God gave his special electing love to Israel (cf. Deut. 7:6-9), but his threats and promises of punishment for unfaithfulness show his fairness and his commitment to justice.

5. God’s actions were not an example of ethnic cleansing.

The Pentateuch (Genesis–Deuteronomy) provides laws for two types of warfare: (1) battles fought against cities outside the Promise Land (see Deut. 20:10–15), and (2) battles fought against cities within the Promised Land (Deut. 20:16–18). The first type allowed for Israel to spare people; the second type did not. This herem practice (the second type of warfare) meant “devotion/consecration to destruction.” As a sacred act fulfilling divine judgment, it is outside our own categories for thinking about warfare. Even though the destruction is commanded in terms of totality, there seems to have been an exception for those who repented, turning to the one true and living God (e.g., Rahab and her family [Josh. 2:9], and the Gibeonites [Josh. 11:19]). What this means is that the reason for the destruction of God’s wicked enemies was precisely because of their rebellion and according to God’s special purposes—not because of their ethnicity. “Ethnic cleansing” and genocide refer to destruction of a people due to their ethnicity, and therefore this would be an inappropriate category for the destruction of the Canaanites.

6. Why was it necessary to remove the Canaanites from the land?

In America we talk about the separation of “church” and “state.” But Israel was a “theocracy,” where church and state were inseparably joined and indistinguishable, such that members of God’s people had both political and religious obligations. To be a citizen of Israel required being faithful to God’s covenant and vice-versa.

The covenant community demanded purity, and egregious violations meant removal (e.g., see Deut. 13:5; 17:7, etc). This also entailed the purity of the land in which they were living as God’s people, and failure to remove the unrepentant from the land meant that the entire nation would be pulled down with the rebellious, resulting in idolatry, injustice, and evil (e.g., Deut. 7:4; 12:29-31)—which sadly proved to be the case all too often under the old covenant.

Christians today are not in a theocracy. We are “sojourners and exiles” (1 Pet. 2:11) with no sacred land in this age. We live in the overlap of the old age and the age to come—“between two places” (in the creation that groans—after the holy-but-temporary Promised Land and awaiting the holy-and-permanent New Heavens and the New Earth). In this age and place we are to respect and submit to the governing authorities placed over us by God (Rom. 13:1–5)—but they are not, and should not be, a part of the church (God’s people called and gathered for Word and sacrament). Furthermore, God’s gift of specific, special revelation to the whole church has now ended (cf. Heb. 1:1–2: “Long ago, at many times and in many ways, God spoke to our fathers by the prophets, but in these last days he has spoken to us by his Son”). These factors combine to ensure that nothing like the destruction of the Canaanites—required for the theocracy of Israel to possess the physical land—is commissioned by God or is permissible for his people today.

7. The destruction of the Canaanites is a picture of the final judgment.

At the end of the age, Christ will come to judge the living and the dead (Acts 10:42; 2 Tim. 4:1; 1 Pet. 4:5), expelling them from the land (the whole earth). That judgment will be just, and it will be complete. That is the day “the Lord Jesus [will be] revealed from heaven with his mighty angels in flaming fire, inflicting vengeance on those who do not know God and on those who do not obey the gospel of our Lord Jesus. They will suffer the punishment of eternal destruction, away from the presence of the Lord and from the glory of his might (2 Thess. 1:8–9). Amazingly enough, Paul asks the Corinthians something they seem to have forgotten, if they once knew it: “Do you not know that the saints will judge the world? (1 Cor. 6:2).

How does this work? What will it look like? I really don’t know. But God’s Word tells us that God’s people will be part of God’s judgment against God’s enemies. In that way, God’s command of the Israelites to carry out his moral judgment against the Canaanites becomes a foreshadowing—a preview, if you will—of the final judgment.

Read in this light, the terrible destruction recorded on the pages of Joshua in God’s Holy Word become not a “problem to solve,” but a wake-up call to all of us—to remain “pure and undefiled before God” (James 1:27), seeking him and his ways, and to faithfully share the gospel with our unbelieving neighbors and the unreached nations. Like Job, we must ultimately refrain from calling God’s goodness and justice into question, putting a hand over our mouth (Job 40:4) and marveling instead at the richness and the mystery of God’s great inscrutable mercy (Eph. 2:4). At the end of the day we will join Moses and the Lamb in singing this song of praise:

“Great and amazing are your deeds,
O Lord God the Almighty!
Just and true are your ways,
O King of the nations!
Who will not fear, O Lord,
and glorify your name?
For you alone are holy.
All nations will come
and worship you,
for your righteous acts have been revealed.” (Rev. 15:3-4)

Posted by Justin Taylor on “Between Two Worlds” blog.
http://thegospelcoalition.org/blogs/justintaylor/2009/09/25/how-could-god-command-genocide-in-the-old-testament/