Though I find this twist gimmicky, they could turn it around into something good. Instead of the endless flashbacks of Bruce remembering the moment his parents were murdered, he could now see the whole thing differently; it could be worse. His father could be a callous, drug addicted bastard who staged his murder in front of his young son, killed his wife and later tried to kill him. With the way things are, at least he has fond memories of his parents to drive him night after night to kick the shit out of criminals.
Batmen you say? Reminds me of the Reign of Supermen. And look how that turned out.
There is no way they would permanently put Wayne out of comission. The whole scenario just seems impossible. I'd think Bob Kane had some fly's shit sized paragraph written into some contract that prevents this.
Also, who would even be fit to fill Wayne's shoes? Tim is the detectice. Dick is the acrobat. Jason is the street fighter. But alone they are just that. Wayne was/is all three of those.