I received the question:

That is not an easy question. Much can be written and has been written on this issue.

First we have to realize that the Bible has been formed over a 1500 year period of God's interaction with his people. There is a lot of "starting where they are and leading them forward and to progress". For example, in the OT polygamy was allowed though the Biblical records clearly look upon it with disfavor but in NT it is no longer allowed.

Also, you will realize in this very chapter of Dt. 20, there is a difference of treatment with the nations in Canaan [verse 16 onwards] and in general [the first verses of the chapter]. You may want to read all of Deuteronomy 20:1-20 to get the context.

My Expositor's Bible Commentary says: These rules for warfare are quite extraordinary. They run counter to much of ancient as well as modern procedures of war, ... Warfare ancient and modern is filled with violence, anguish and inhumanity. These directions given to Israel must be measured relative to the war tactics of the world they lived in and to the heineousness of the sins of the cultures of Canaan.

I hope that gives a reasonable background picture.

Now, why the wholesale distruction of the tribes in Canaan? Have a look at Glen Miller's fantastic Christian Thinktank, who also has an article on destruction of the Canaanites.

Let me also include a shorter piece of a discussion I recently had with a Muslim on this issue of cruelty. Maybe these short thoughts will also be helpful. This is the tail end of a longer discussion, so not everything might make complete sense, but I hope enough to be somewhat beneficial.

When he brought up the Amalekites etc. I asked this Muslim to look at Sura 18:60-82 and particularly verses 74-76 & 80-81 and so the following is his response and my reply to him in return.

Subject: Re: Amalekite Massacre 

? G: I assume the problem Jochen has in mind is the fact that we see this
? servant of God killing a presumably innocent young man.  
? G: As the passage continues, Khidr later explains what he did. 18:81-82 "And
? as for the lad, his parents were believers and We feared lest he should
? oppress them by rebellion and disbelief. And we intended that their Lord
? should change him for them for one better in purity and nearer to mercy."
? Allahu alim. I would rather not treat my own speculations about the Quran as
? established interpretations. But it looks as if the lad wasn't innocent.
? Khidr had a special knowlege about the young man and knew that he would cause
? alot of trouble for his parents. 

The issue is that he *is* innocent at this time but would be causing trouble
in the future.

? (And recall that in the Old Testament as
? well, rebelliousness towards ones parents is a capital offense).

But only for committed sin, not for potential sin in this case.

? This seems different from the case of the Amalekites (and remember that we
? are not just talking about the Amalekites but genocide against *many*
? different groups who originally inhabited the land of Canaan) this seems
? different because this is only one person while the in the Biblical case we
? must be talking about thousands of people. So first there is the issue of
? magnitude. But secondly, the Quran gives a specific reason for why this one
? person was killed. He wasn't innocent. It is explained that he would grow up
? to be a bad seed. But in the case of the Biblical massacre it is far from
? obvious that every single one of the babies which the Israelites killed was
? going to grow up evil.

I don't think that quantity makes a difference in principle in this argument.
If God can sanction/command killing one person who might become evil, then
he can do so with several or even many. The question is if God can do so,
is allowed to do so, and if a book that says he does is to be rejected.

Whether he does it once, sometimes, many times, clustered with many at
a particular time, or spreads out the many over a long time, is not changing
the quality of the argument. The validity is not depending on the number
of times it is executed.

It was far from obvious to Moses in the Qur'an that this was justified.
Moses was horrified at Khidr's action.

Anyway, before you go on, please explain how on earth you can accept this
in the Qur'an, but not in the Bible, and also read the web page by Glen
Miller on the subject. 

In Genesis already, God tells to Abraham that he will give him and his 
descendents this land, but only in about 400 years, and the evilness of
its inhabitants has not yet reached its full measure. God has indeed 
great patience and compassion and sends prophets to live among them
and speak about the one true God. But they continue and increase in 
their abomination and then when God finally executes judgment, 400
years later for most of those tribes and nearly 900 years later in
the case of the Amalekites, is he not merciful and forbearing and 
just? By now we do know from archeology much of the atrocities committed 
by these peoples, of idolatery combined with child sacrifices, sexual 
orgies and more. This was the general lifestyle of those people as 
unearthed by archeology.

Is God allowed to judge a nation that persists in evil for many hundreds
of years? Do you think those children would have for some miracle been
completely different than their parents and society?

And why did Khidr then not kidnap the innocent youth and bring him in
a different environment and educate him to be good, instead of just
killing him?

And then, did Khidr even have a direct commandment from God to do so?
God said so through Samuel. But did God give a command to Khidr or did
he do this out of his own knowledge or intuition? After all, maybe God
wanted to be merciful like with the Amalekites for some more time 
even though they would be doing more evil?

It is all not so easy, ...

Also have a look at this hadiths about the al-Khidr story: Bukhari, Volume 6, Book 60, Number 249 - 251.

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