Well...how about a series about war between the mirror universe and the normal universe. Told from the mirror universe POV. I think you couldnt get much darker for a trek series as a whole. Not sure if that would sell of course. Or how about this:
A trek series taking place on two entirely different ships. One ship out exploring, while the other ship is a secret ship working for section 31....for the dark stuff. The actions of both ships influence each other...although they rarely interact directly. Switch between the ships per episode. That way you could have a trek thats darker AND lighter at the same time. And instead of using big season arcs the show should use mini arcs of three or four episodes.
Dont know if that would sell either. Well..,a way to satisfy boths camps of lighter and darker would have to be found.
Interesting, sounds like the fringe tv series.