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First, just as a beginning, it should be noted that the Israelites were not always commanded to annihilate all their enemies, only certain ones. The reasons will be suggested below.
Second, if there is plenty of evidence that the Bible is God’s Word, and there is, then for finite man to deny the Bible because he doesn’t like something or does not understand the reasons for some of what it teaches, is nothing short of arrogant rebellion against an infinite God who has revealed Himself. For evidence that the Bible is God’s Word, may I suggest Josh McDowell’s books, Evidence that Demands a Verdict and More Evidence that Demands A Verdict.
With this in mind, may I also suggest that there are many more and greater difficulties in rejecting the Bible and its teaching than there are in accepting Scripture with its so-called difficulties. Why is this so?
(1) It seems to me that we face greater difficulties in rejecting the Bible because of the mountain of evidence that the Bible is unique and true as supported by archaeology, fulfilled prophecies, its unity and continuity from Genesis to Revelation, and by the way it has changed lives and even civilization to name just a few evidences. For some outstanding evidence of the impact the Bible and Jesus Christ have made on humanity, may I suggest two books: What If Jesus Had Never Been Born? and What If the Bible Had Never been Written? by James Kennedy and Jerry Newcombe. I have not read the second book as yet, but I am certain the second book does what the first book does. They both trace the impact Christ and the Bible have made on the world by contrasting or comparing those places that have not been touched by the Scripture and by faith in Christ.
(2) Then also, we should consider the fact that the so-called difficulties fall into different categories, each of which needs to be considered. Let me just suggest a couple that come to mind: (a) Some difficulties are only apparent and exist because of an ignorance of certain facts or a lack of understanding with man pitting his finite mind against God’s (see Isa. 55:8-9). (b) Then there is what we can call the moral twist problem in man’s heart. Man is too often looking for an excuse to reason away the Bible or reject it so he can proceed independently of God to pursue his own unrighteous agendas. As Christ put it, he doesn’t want to come to the light because his deeds are evil (see John 3:19-21). And by the way, evil deeds according to the Bible do not just include what men often consider immoral issues. They include man’s attempts to be religious, to solve his own personal and social problems, and be good by his own works, and all of this independently of God.
(3) Just because we can’t seem to solve a problem or understand something or because it seems contradictory to us does not means it is unsolvable or not true. The slaughter of Israel’s enemies at the command of God may seem inconsistent with a loving God, but it was really an act of love for Israel and others due to the moral condition of these nations which included child sacrifice as archaeology has clearly shown. The degradation of these people was horrible. Further, God, who knows the hearts of men and what they will and will not do, was acting on the basis of that knowledge. Thus, God ordered their judgment in order to protect Israel and their development as a nation, for it was through them that God would give the Savior of the world, the Lord Jesus Christ. Further, God had waited some 400 years before ordering their destruction until their iniquity became complete.
(4) Also, consider this. Man often wants to know how to harmonize God’s ‘justice, holiness and truth’ with His ‘love, mercy, and compassion,’ We seldom reverse this, however, and want to know how to harmonize His ‘love, mercy and compassion’ with His ‘justice, holiness and truth.’ Instead of wondering why a loving, merciful, and compassionate God destroyed the Canaanites or the Amalekites, why not wonder why a just, holy and true God was patient with them for such a long time considering their totally degraded behavior. Indeed, in view of the absolute holy character of God as presented in the Bible, why does he bear with any of us? Why was He willing to send His Son to die for our sin so that they who believe on Christ might be saved? This is the mystery which finds its answer in God’s love.
Furthermore, I find it strange that men and women today who challenge Christianity, using as one of their reasons the slaughter of men, women, and children, are often supportive of abortion which is nothing less that the true slaughter of innocent children by the millions.
(5) The book of Revelation teaches Christ will come to earth and literally destroy millions because of the rebellion and unbelief of man’s heart. In fact, the tribulation period, which is described for us in Revelation 6-19, will among other things, demonstrate the true nature of man and just what lengths he will go to in his sin and rebellion when left to himself. Christ spoke of this time in Matthew 24. So the Old Testament is not alone in demonstrating God’s wrath and judgment against sin.
(6) Another argument that is important to consider is Jesus Christ’s own understanding and attitude toward the Bible. Christ clearly believed in the Old Testament was God’s inspired Word, that it was accurate, historical, good and righteous, and that not even the smallest Hebrew letter or stroke of the letters of the Old Testament would pass away until all was fulfilled. For instance, He said:
17 “Do not think that I came to abolish the Law or the Prophets; I did not come to abolish, but to fulfill. 18 “For truly I say to you, until heaven and earth pass away, not the smallest letter or stroke shall pass away from the Law, until all is accomplished.
Why is this important? It is important because of the resurrection of Christ. If Christ was raised from the dead, and the evidence that He did is awesome, then this marks Him out as not only unique, but it validates His claims and that of the Bible’s claim about Him. This means that there is incontestable evidence that He is truly the Son of God or God who became flesh and died for our sin. If this is so, then what He believed and said had to be true. For instance, compare the following verses:
Romans 1:1-4. Paul, a bond-servant of Christ Jesus, called as an apostle, set apart for the gospel of God, 2 which He promised beforehand through His prophets in the holy Scriptures, 3 concerning His Son, who was born of a descendant of David according to the flesh, 4 who was declared the Son of God with power by the resurrection from the dead, according to the Spirit of holiness, Jesus Christ our Lord,
Acts 17:30-31. Therefore having overlooked the times of ignorance, God is now declaring to men that all everywhere should repent, 31 because He has fixed a day in which He will judge the world in righteousness through a Man whom He has appointed, having furnished proof to all men by raising Him from the dead.”
For studies dealing with evidences for the resurrection of Christ, see the articles on our web site in the “Bible Studies / Theology / Christology” section.
Finally, below I have included a short section from Norman Geisler’s book, A Popular Survey of the Old Testament, that directly addresses this issue which might help here.
A Moral Problem—the slaughter of the Canaanites (Josh 6, 8, 10).
Israel was commanded by God to completely exterminate the Canaanite inhabitants of the land including men, women, and children. This has been called a primitive and barbaric act of murder perpetrated on innocent lives.
Several factors must be kept in mind in viewing this situation. (1) There is a difference between murder and justifiable killing. Murder involves intentional and malicious hatred which leads to life-taking. On the other hand, the Bible speaks of permissible life-taking in capital punishment (Gen. 9:), in self defense (Exod. 22:2), and in a justifiable war (Gen. 14). (2) The Canaanites were by no means innocent. They were a people cursed of God from their very beginning (Gen. 9:25). They were a vile people who practiced the basest forms of immorality. God described their sin vividly in these words, “I punished its iniquity, and the land vomited out its inhabitants” (Lev. 18:25). (3) Further, the innocent people of the land were not slaughtered. The story of Sodom and Gomorrah clearly demonstrates that God would save a whole city for ten righteous people (Gen. 18:22f.). In that incident, when God could not find ten righteous people, He took the four or five righteous ones out of the place so as not to destroy them with the wicked (Gen. 19:15). On another occasion God saved some thirty-two thousand people who were morally pure (Num. 31:35). Another notable example is Rahab, whom God saved because she believed (cf. Heb. 11:31). (4) God waited patiently for hundreds of years, giving the wicked inhabitants of Canaan time to repent (cf. 2 Peter 3:9) before He finally decided to destroy them (Gen. 15:16). When their iniquity was “full,” divine judgment fell. God’s judgment was akin to surgery for cancer or amputation of a leg as the only way to save the rest of a sick body. Just as cancer or gangrene contaminates the physical body, those elements in a society—if their evil is left to fester—will completely contaminate the rest of society. (5) Finally, the battle confronting Israel was not simply a religious war; it was a theocratic war. Israel was directly ruled by God and the extermination was God’s direct command (cf. Exod. 23:27-30; Deut. 7:3-6; Josh. 8:24-26). No other nation either before or after Israel has been a theocracy. Thus, those commands were unique. Israel as a theocracy was an instrument of judgment in the hands of God. (Norman L. Geisler, A Popular Survey of the Old Testament, Baker Book House, Grand Rapids, 1977, pp. 99-100.)