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.
This is one of those kinds of things Living Missions could fix. Set up an alternate system for folks to just privately run missions for friends and Fleet members that aren't accessible unless someone's explicitly invited. I keep going back to SWG's Storyteller system. There all missions were custom built to be run for particular groups by real, live, player-GMs. If you wanted in, you'd join the GM's part or one of his assistant's parties.
This led to missions and whole story arcs around certain characters/guilds/factions that changed and evolved over time and based on the player-characters actual decisions/choices in the missions. Like, real roleplaying stuff.
This, seriously, builds communities. If you hear that Fleet X runs great adventures, posts pics and roleplay logs, and the like you're going to want to get to know Fleet X even if you don't join. Maybe get involved as a friend of the guild and learn how to do your own missions. Characters and stories cross-pollinate between fleets and build contexts broader than any single guild.
If we're stuck with static, scripted, missions and only ones that the general public will enjoy/can make sense of as generic STO missions then that makes it impossible for player-characters to be the driving force in any player-run storyarc.