Okay, so my take on this is that the "rule" for becoming a "god" is talking about how Sanae is the only one semi-aware that she's in a "game", through Continues and what-not. She knows that as long as she's "destroying evil", she's fulfilling her role as the Heroine, and thusly can't lose, no matter how many times she's defeated.
However, when she's fulfilling that role, it's not her who's in control, but the Player, i.e. us. And we, as players, always attempt to mercilessly beat down our opposition, because to us it's just a game where defeating the opponents is the goal.
Sanae is only dimly aware of what's going on when she's being "The Heroine", and it feels like a dream where everything you do makes some kind of logic, no matter how twisted. But when she/we defeat the Final Boss, Hijiri, the Player has no reason to stick around, and Sanae is back in control, now fully aware of what she has done. Cue the regret.
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