In the first five books of the OT, there are at least 21 times where people were killed directly or ordered to be killed by God. Yet God said, "Do not kill." Take the Midianites in Numbers 31, for example. As I see it, between 100,000 and 160,000 Midianites were massacred because one Israelite committed adultery with a Midianite woman (Numbers 25:6). Huh? Not to mention the fact that in fighting the approximately 60,000 Midianite males not a single of the 12,000 Israelite soldiers was killed, which to me, smacks of mythology.) How do you deal with this?
Let's begin with the emotional element of your question. Yes, God said, "Do not murder." Yet since even God takes life (in both testaments) and is the final judge of every human being, it cannot be inherently immoral to take a life. (Focus on the word inherently.) I have addressed this issue elsewhere at the website, so only a brief explanation will be provided here. Murder and killing are apparently different things. Taking a life is not the definition of murder. The Oxford English Dictionary defines murder as "the most heinous kind of criminal killing; illegal killing with malice aforethought." In western culture, we as a society are becoming more and more adverse to violence--which is commendable. And yet we are also becoming more and more adverse to penalties for crime, adverse to character and behavior modification for children (whose parents are often expected to "obey" the law!), and adverse to tough discipline in our own lives. I think these social factors condition us and make it more difficult for us to weigh the biblical evidence objectively.
Secondly, killing was commanded in the O.T. in certain instances, but never in the N.T. That is because in the O.T. church and state were one, whereas under the new covenant they are separate. The church was not the Roman government. This may sound obvious, but it needs to be emphasized, otherwise we'll end up making false comparisons between the covenants.
In the O.T., there were a number of death penalties. But there was a different category of taking of life commanded by God. That was in fact extermination of the enemies in the Promised Land. Deuteronomy 9:4-6, a passage I have often steered people towards, shows that this is not just a matter of moral superiority. Deuteronomy 20 is a very helpful chapter, since it distinguishes between nations in Canaan and nations outside. Please read it.
Of course the Midianites were based far from Israel, while the Moabites (Numbers 25) were nearer, although even in the book of Genesis we find Midianite/Ishmaelite nomads trading broadly. We also encounter Midian in Gideon's battle (Judges 7). Sometimes they were present in the Holy Land, at other times at some distance from it.
Now let's move to the book of Numbers. As for Numbers 25, it was not a single instance of sexual immorality that led to the war against Midian. (Moab and Midian appear to have been allies in the battle against Israel.) The example highlighted in this chapter was meant to show how prevalent--and bold--sexual sin had become, as the Israelites imitated surrounding society. The nation as a whole was on the brink of apostasy. (And this hardly the first time, as the reader of Numbers is reminded!)
Nor was it only the Midianites who suffered; the text says there was first the plague against the Israelites, and many thousands died (Numbers 25:9). Sin is sin, whoever commits it, and God's people are certainly not exempt from its consequences.
In Numbers 31, which you refer to, I see no record of the numbers of deaths on the Israelite side. Numbers 31:49 refers to the thoroughness of the census, not battle fatalities, if I am reading the text correctly. Nor does the text indicate a single battle (12,000 against 60,000, say). Rather, the Israelites went from town to town. Few towns would have been larger than 5000 or 10,000. I see no exaggeration here. If you have read ancient history, you know that some writers do stretch the truth, and the Bible is impressively modest by comparison.
Last, it must be emphasized that only God has the right to judge. The Torah makes it abundantly clear that what the Lord was doing through Israel was exceptional in nature. Generations earlier, since "the sin of the Amorites had not reached its full measure" (Genesis 15:16), the Lord still extended hope and mercy to the non-Israelites of the Holy Land. Yet as time passed and society became ever more decrepit, the Lord had no choice but to decree destruction. The conquest of Canaan, in this light, may be viewed as a surgical operation.
Look at it from the eternal perspective. When the Canaanites' fate had been sealed, they were under God's judgment. None would be saved (or almost none -- Rahab and family are obvious exceptions). If they affected (contaminated) the Israelites, then not only the pagans would be lost, but the Israelites as well. In fact, this is basically what did happen; the OT record makes clear that most Israelites fell spiritually through compromise with the pagans. They shared husbands and wives, religions, culture, and morals. Had the Israelites more fully followed God in dealing decisively with the pagans, far more Israelites would have been right with God. (And in all likelihood far more pagans, influenced by the example of Israel, would have converted to Judaism than the small number who did convert in OT times.) May it not be that the Lord is optimizing (maximizing) the number of people who will eventually make it to heaven?
Hopefully by being aware of our emotional and social conditioning, and then approaching the question from a variety of angles, we are able to arrive at satisfactory conclusions. Your question is a great one because it is honest and because it attempts to wrestle with the text itself. Keep asking questions, and don't settle for cheap answers. On the other hand, remember the Lord and all he has done in your life, and try to interpret his actions in ancient times in light of what you know to be true of God as he has worked in your own life.
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