Makes sense about the origin happening before Bruce comes back and Batman comes to save Gotham.
However, I feel like he hasn't turned yet, even if The Joker card is there. Some serial killers have been known to leave their mark at the crime scene whether it be an item like a playing card or a rose, a piece of hair, or a note.
If Nolan was going to use "The Killing Joke" he'd have to either skip the whole origin and find different pages and panels to use, or he'd have to switch it where the origin happened long before Batman and Bruce, where Gordon was taking the place of Batman as the city's defender, but then blew it when he let the criminal jump into a vat of chemicals instead of arresting him.