My opinion's mixed on the ending. If the show goes through with it, its one of the most daring things a television show has ever done--but, the show loses its raison d'etre. On the other hand, pulling back and "J.R."-ifying it in some way would be downright cowardly and cheesy. I guess we'll see.
He's not going anywhere. Without him there is no show. It's a dramatic plot element. With Tony laid up there is a power struggle in the works. Fat Gay Guy is already making noise about where he wants to be and Chris has his own ideas. I see some interesting stuff leading up the season intermission.
I did see one reviewer suggest that he could linger in a coma or even die and still narate as in a Shakesperean choir.
Either way, Junior is toast, whacked or shipped to an old age home a la Livia.