And you're saying no good person ever has bad thoughts? You'll be absolutely wrong; everyone does, but normal people have inhibitors called a conscience and principles that guide their actual actions. Artificially remove people's inhibitors (like excessive alcohol) and they will be completely different people.And you're forgetting that they explicitly stated that if she hadn't already had such thoughts that the Goddess wouldn't have been able to take her over and do so.
In summary:
THIS FLASHBACK HAS BEEN GOING FOR TEN THOUSAND YEARS CAN WE MOVE THE FUCK ON PLEASE