Plus, it's not like people are out there thinking that in the next two years I am only going to see one Sci-Fi movie, because the same guy is directing both.
That's it in a nutshell. In what universe does the average person decide that they can only see one movie with "STAR" in the title, directed by J. J. Abrams, over the course of a few years?
Let's be honest: 99.9999% of us are going to see both movies, regardless of who is directing them. So where's harm?
More importantly: a successful STAR TREK movie does not hurt STAR WARS, and vise versa, unless they're both opening within a few weeks of each other. Good scifi movies just make people want more good scifi movies.