I think it comes from the Old Testament times. When God saw that the whole world was sinning, He let loose the flood, but saved the clean souls of Noah and his family. When Sodom and Gommorah were showed to be cities of evil, He destroyed them after giving warning to Lot.
When we get to Jesus, I think of it as God trying a new stratagy. Instead of killing everyone, he sent Jesus in human form in order to teach humanity about Him, and then die in order to cleanse the sins of the world.
I'm not a particularly religious person, so I'm just posting what I have thought about with this question.
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