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"Post-fall Hannibal would kill Chilton" No he wouldn't.
Hannibal wants Chilton alive, surviving more than living, cause that's the lesson Chilton needed to learn.
Chilton always believed he was in charge of people, that he had power over them. When he truly didn't.
He felt like he had power over the fake Chesapeake ripper, and for that he got his organs removed while awake. He thought he had power over Will, and the fact that Hannibal was the real Chesapeake ripper, and that got him framed and shot by Miriam. Lastly, he thought he had power over the Great Red Dragon, and that got him burnt alive.
He has suffered time and time again, every time because he went against Hannibal, and believed he has power over the situation. But he never truly did.
So he would keep him alive, as a cruel reminder that he is powerless, and that he would be dead if Hannibal wanted to.