Yeah, either they have to come up with someone else to play the Joker, or just write him out of any subsequent movies. I don't know the storyline well enough to know if he's one of the recurring characters. But Heath was under enough makeup that I think they could bring someone else in to play the part; that actor would just do it a little differently.
I see they're introducing Harvey Dent in this movie, so they're likely setting up his character for the next one.