Even if JJ has moved on to a better-paying customer who drives a fancier car and pours a better brand of champagne, I'm sure Star Trek will continue to be lucrative enough that Paramount will continue the movie franchise with a different director.
Both Star Trek and Star Wars have survived the worst that can be thrown at them (Star Wars in particular, yeesh) so there's no need to fret about either. They're touch sumbitches.