Genocide in the bible

http://www.reasonablefaith.org/slaughter-of-the-canaanites

http://thegospelcoalition.org/blogs/justintaylor/2009/09/25/how-could-god-command-genocide-in-the-old-testament/

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)

Thanks to David Reimer, James Grant, Andy Naselli, and Jim Hamilton for reading a draft of this answer and offering counsel and encouragement. I also want to acknowledge the discussion in the Introduction to the book of Joshua in the ESV Study Bible, which was very helpful in thinking through this issue.

http://carm.org/god-of-old-testament-a-monster

The Amalekites were particularly cowardly in their attacks on Israel and would deliberately murder the weak and elderly who sometimes lagged behind the core group of Israelites who were making their way to the land promised them by God (cf. Deut. 25:17-19). The book of Judges (6:3-5) records that they consistently allied themselves with other nations to commit genocide against Israel.

Amazingly, God chose not to destroy the Amalekites until some 400 years had elapsed from their first sinful acts against His people. Such an incredibly long period of time shows the patience of God and dispels any notion that God is quick tempered and rushes to judgment against those who are sinning before Him.

Scripture also contains God’s warnings to the Kenites, who were a people living among the Amalekites, to depart so they would not be caught up in the coming judgment (cf. 1 Sam. 15:6). Such a warning had to have also been heard by the Amalekites, and it is reasonable to assume they could have fled the land as well, but they chose not to.

Although God commanded Saul to completely destroy the Amalekites, he disobeyed and did not completely do as he was told (cf. 1 Sam. 15:9-26). Some were allowed to live, an outcome that ultimately resulted in another attempt of genocide upon Israel. The book of Esther records that a man named Haman – who was of Amalek descent – tried to have all the Jews killed in the land of Persia, but he was ultimately stopped by Queen Esther herself.

we see a distinct pattern emerging from the judgments brought by God upon various peoples:

God declares an annihilation form of judgment to stamp out a cancer
The judgments are for public recognition of extreme sin
Judgment is preceded by warning and/or long periods of exposure to the truth and time to repent
Any and all ‘innocent’ adults are given a way of escape with their families; sometimes all given a way to avoid judgment via repentance or leaving a particular region. It should also be noted that expulsion from a land was the most common judgment, not extermination. This pattern goes all the way back to the ejection of Adam and Eve from the Garden of Eden (cf. Gen. 3:24)
Someone is almost always saved (redeemed) from the evil culture
The judgment of God falls

Far from being innocent, the objects of God’s judgments were involved in gross sin and committed acts of great barbarism, such as ritualistically burning their own children to death as offerings to their false gods. Amazingly, instead of immediately destroying the peoples involved in such things, the actual opposite is found: the Scripture conveys that God had incredible patience and waited until the full measure of their deeds were completed. For example, while speaking to Abraham about the future exodus of Israel from Egypt, God says the following about the Amorite people: "Then in the fourth generation they will return here, for the iniquity of the Amorite is not yet complete” (Gen 15:15).

“By setting such strong, harsh dichotomies God taught Israel that any assimilation to pagan idolatry is intolerable. It was His way of preserving Israel’s spiritual health and posterity. God knew that if these Canaanite children were allowed to live, they would spell the undoing of Israel. The killing of the Canaanite children not only served to prevent assimilation to Canaanite identity but also served as a shattering, tangible illustration of Israel’s being set exclusively apart for God.”
― William Lane Craig