The Sixth Commandment, found in Exodus 20:13 and Deuteronomy 5:17 is variously rendered as "You shall not murder" or "You shall not kill".
Yet there are various places in the Bible where God commands or seems to approve of murder. Not all killing is murder, of course, but in some cases it can be described as little else. Here's 1 Samuel 15:1-3:
Not only does this instruction to slaughter women and children seem to contradict the Sixth Commandment, it also seems totally repellent in its own right, and at odds with the idea of a benevolent God.
These words are actually spoken by Samuel. Is it possible to argue that they are not really coming from God? I do not think so. The blogger Free Northerner puts it well:
Well, quite. Regardless of whether the book of Samuel has a divine or purely man-made origin, the author of the text certainly intends you to understand that those really were the words of God.
A lot of apologists make much of the fact that the Amalekites were chronically at war with the Israelites for hundreds of years, quite probably inflicting similar horrors on them. But the children would clearly be blameless in that matter, and the women mostly so; and obviously nobody is responsible for events that occurred before their birth.
The strongest inerrantist argument I'm aware of is roughly as follows:
My problem is, an omnipotent, omniscient God always has other options. Instead of these murders, I suggest that an omnipotent, omniscient God could come up with subtle solutions to "the Amalekite problem" involving neither gross manifestations of divine power, nor evil atrocities - and being benevolent, he would prefer such a solution.
Morality, it is often said, comes from God, and so whatever he commands is good, and what he prohibits is evil, and this is simply what the words mean. This is sometimes called the Divine Command Theory of morality. Problems for this view have existed since Plato.
A lot could be said about this, but (as I see it) the core problem is that the Divine Command Theory removes most of the meaning from the words good and evil. For example:
Such definitions of good and evil rob the terms of any moral force.
Under a certain view, children who die young automatically go to Heaven. In that case, the Israelites were not really harming them, all things considered. Indeed, they were saving them from the chance of Hell. I suppose one could hold this view, but it seems to prove too much... At birth, everyone has a strong chance of going to Hell (assuming it really exists) so killing a child is always good for that child, on this view. I would discourage you from thinking along these lines, to put it mildly.
Instead, I will continue to take the view that killing children is bad for the children. In any case, this doesn't deal with the killing of women in 1 Samuel, and I've even heard unconfirmed rumours that men are people too. The Amalekite men could hardly all be guilty of war crimes.
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Other verses that involve the killing of innocents (apparently with God's approval) include Numbers 31:17-18, Deuteronomy 2:33-34, Joshua 6:21, Psalm 137:9, and many more. There are lists on the internet for those so inclined. In most cases God's approval is only implied (for example, Joshua 6:27 suggests God endorses the earlier massacre, and Psalm 137 is more of a prophecy than an actual event) but in 1 Samuel 15 the killings are explicitly ordered by God, making it the strongest example.