Well for sure it's certain he will indeed be on as producer but yes he might still have a chance to come back, and direct the next installment of the Trek series.
All he would have to do is jump right back into it after he finished STAR WARS. When the news broke last night most fans thought to themselves well what's the future hold for Star Trek now? The answer didn't take long.
Well now we know that Abrams is set to serve as a producer on both the third Star Trek movie and the next Mission Impossible (presumably under his 'Bad Robot' banner). Today it was confirmed by Rob Moore Vice Chairman of Paramount Studios. "J.J. will continue to develop projects for us including a new ‘Mission: Impossible,’ and he is committed to produce another ‘Star Trek," he said. Of course, this doesn't necessarily mean that Abrams won't direct the third installment like I said all he would have to do is just go from Star Wars back to Star Trek, and continue forward if he chose too.