This is a great example of Rabbi insistence that the Bible is meant to studied, not read. This whole thing is complicated, so let's begin with noting when the Command to "wipe them out" and the claim they were "wiped out" occurs the same way in other cultures of this day and age. We read it as every single person was killed, when even outside Biblical cultures this hyperbole meant they were the victors. (There are verse that those who just before had been wiped out, reappeared in the narrative.)
By God's Law the Israelites were to offer their adversaries choices. If the adversaries chose war, only then the situation became, win at any and all costs (or mow down everyone).
The Bible relates accounts where war was chosen so the command was to win at any cost, yet one of the leaders would choose mercy instead--and God always celebrated these acts of mercy. He did not see it as an act of disobedience.
Using this as an analogy, this is basically the lesson inherent in the Bible: alang and Meriweather were having a serious disagreement. God commanded alang to kill Meriweather, to wipe her out. This sets things in motion for alang. Clearly, God sides with alang against Meriweather.
So, according to law, alang approaches Meriweather and asks her to resolve the difference peaceably. She refuses. So alang asks her to turn away from attacking him. She refuses. She tells alang, "I choose war." alang considers this, knowing that if he accepts the offer of war, he is going to win because Meriweather is rather puny and knows little about war. So alang forgives Meriweather her bullheadedness and God is pleased with alang. (Not so much with Meriweather. He sends a flood to keep her occupied with other matters. Just kidding.

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I am pointing out the steps that were taken before war occurred. People of the day were fully aware of these steps. It is like people in the far future only seeing one bit of information, that bit being, "The President was impeached." We of this time know the steps to impeachment, but those will be long since forgotten if most of our history is destroyed, giving rise to conclusions a President could be impeached in a minute. Just like we know what we really mean when we declare, "We wiped the floor with them."