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

[The Industrial Atheist]

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 he"s omniscient, and knew that everyone would become evil and have to be killed.  The morality just brings tears to your eyes, don't it?

Doesn't that mess with free will?