films have never revolved around one director or cast so why should the Abrams-era movies be any different? If J.J. is too tired or busy (or both) to helm the third film then he and Paramount will nail down the best director they can for a reasonable price. That's Hollywood. Paramount made....what? Almost $400 million worldwide on Trek '09 and is banking on the new film to make big bucks and be a runaway summer hit?
They'll find somebody else if they have to. Hollywood is full of directors who wouldn't mind helming a major pop culture franchise, even if just for one movie.