There will be a third nuTrek film, but with the movie under performing Paramount's expectations, and the studio higher ups being irked by the Star Wars thing, there's still hope JJ won't be doing the next movie.
Really though, Abram's isn't as big of a problem as Orci. That's the guy that we really need to get away from Trek.
produce and oversee the next Star Trek
Orci is not going anywhere.
Period, full stop.