I just don't really think the risk of abuse is that great. It could happen, but it's not that likely, and the damage is limited if it does. After all, nothing can stop someone from posting pedophile stories online, even if they can't do it in STO. So, it's not like we can stop them from being that way. I guess I can understand that Cryptic might be concerned about that sort of thing though as it could open them up to lawsuits, or at the very least bad publicity.
I don't really care if private missions are allowed as I don't plan to make one, but I do think it would be easier for all of us if a mission could at least be flagged as private, or special or something along those lines. Even if others could still actually play, it would remove some unnecessary clutter in the mission search. But maybe that's more along the lines of improving the search, rather than private missions per se.