Their moral instincts, and the positive/negative reinforcement to obey them (i.e. pleasure or guilt), keep existing regardless of external laws.

Right, we agree on that. But if the apostate thereafter has no reason to regard themselves as morally responsible, then their moral behavior is no longer fully rational. They're sort of going through the motions.

Which might not be a good reason to murder someone according to you, with your normal neurobiology–you would content yourself with fuming and making rude comments about him to your friends–but she considers it a good reason, because her mental 'brakes' are off."

The question here isn't about good vs. bad reasons, but between admissible vs. inadmissible reasons. Hearsay is often a bad reason to believe that Peter shot Paul, but it is a reason. It counts as evidence. If that's all you have, then you're not reasoning well, but you are reasoning. The number of planets orbiting the star furthest from the sun is not a reason to believe Peter shot Paul. It's not that it's a bad reason. It's just totally inadmissible. If that's all you have, then you're not reasoning badly, you're just not reasoning at all.