I never expected Abrams to direct a third Trek film and I'm surprised he's even directing Into Darkness. He has a long history of setting things up and then moving on so that others can take over.
Personally I don't think it's a big deal and in his shoes, I'd probably do the same thing. Who in their right mind would pass up the opportunity to direct films in two of the biggest sci-fi franchises to have ever existed. Unless he has some sort of burning desire to direct a third Trek Film, I say if they make the offer than he should most certainly take it.