I think the lack of Klingon missions in Star Trek Online could be due to a lack of thinking outside the box by creators of missions. If you're going to play what is the equivalent of "bad guys" (at least in the eyes of the Federation and Starfleet) then those missions should involve doing things that might reflect that view. It's fine to assault bunches of Starfleet officers that are milling around on a planet but Klingons would not stop there. Civilians would also be taking dirt naps, property would be destroyed, people would be subdued and perhaps shipped off to the mines of some moon somewhere. The Klingons would be doing things that further their interests no matter how morally repugnant these things were to the Feds.
If STO is not going to push the envelope for these kinds of "adult" missions because they are afraid they are going to offend people, then don't have a faction that is, in effect, the "bad guy" of the game.