I know it's different. Nolan takes a realistic, or hyper realistic or quasirealistic, however you want to see it, take on the batman universe.
In Knightfall, as a side effect of a psychic battle against her brother, a doctor healed Wayne's back with her powers. To rehabilitate his skills, Bruce asks the famed assassin Lady Shiva to retrain him. Instead, Shiva pits Bruce against several vengeful expert martial artists. Shiva's caveat is that these attacks will continue indefinitely until Bruce Wayne breaks his vow to never kill. Finally, in the midst of another attack, Bruce feigns using the "Leopard Blow" fatal maneuver Shiva had taught him, leaving his would-be assailant apparently dead. Shiva finally declares him worthy of fighting her at some point in the future.
Given that, I just don't see how a normal healing process with additional training within the prison over the course of 6 months is in any way out of tone with the rest of the films. He took the same basic idea and executed it in a more realistic way, as he had done with all his batman films. And Batman recovering from his injuries this way is no less faithful to Batman's comic roots than twoface was.
