How do religious folks reconcile violent concepts in "peaceful" Abrahamic religions?

[The Industrial Atheist]

Al Qaeda used a similar argument to justify Muslim casualties. I doubt that peoples far away from the Jews knew anything about Yahweh. But what I meant is-Wouldn't it be better to make personal appearances to these peoples before things got so bad rather than just let things go to pot and then kill everyone? Wouldn't that be the more moral solution for a being that can see the future?

The Muslim example does not apply. This is a decision God made (with the benefit of omniscience) and God carried out. 

God would be aware of the counterfactuals of appearing to them and entreating them to turn from their wicked ways. It appears wiping them all out and starting with a new generation that would honor God was the most moral thing to do. If God weighs all the future lives, doing nothing would result in far far more people in Hell, perhaps an intervention would reduce that number, but again, eternal perspective.

So basically god did the right thing because he always does the right thing because he's god. Like Li'l Bush. "Circular reasoning. Means it works."