User blog comment:Nightband/Season Seven Plot Hole?/@comment-10603955-20121214011240/@comment-10603955-20121214020200

Also...

Think about, if the world was really some computer, there is bound to be some glitches and virus. Forcing the maker of the network/software to make recycle bins, vaccines, and fire walls.

This is a description of how Supernatural's God is, he didn't find the leviathans violent at first because he probably missed a few things. So He fixed the bugs with mankind and stuff after that.