Hmmm I'm not sure about religious texts being morally dubious or evil for that matter since faith is practically one of the first things a believer is required to have. If one does not have faith that the scripts didn't come from the word of God(s), then it's pointless to mull over.
What? That makes no sense. You can't just generalize Atheists. Not every Atheist thinks the same. Although, I do agree about Dawkins. He insists that indoctrination on a child is worse than sexual abuse. Weirdo.
I'd say the worst one is "God can make a rock that he himself can't lift", implying that the Monotheistic God is a Finite being rather than Eternal and Omniscient.
The second scenario will inevitably bring more problems. Humanity hasn't learned how to move past violence, discrimination, and ignorance. Kill those three first, and I'll consider that option.