I have wondered about this a lot myself, but can't make much sense of this:
And then Vivec withdrew into the hidden places and found the darkest mothers of the Morag Tong, taking them all to wife and filling them with undusted loyalty that tasted of summer salt. They became as black queens, screaming live with a hundred murderous sons, a thousand murderous arms, and a hundred thousand murderous hands, one vast moving event of thrusting-kill-laughter in alleys, palaces, workshops, cities and secret halls. Their movements among the holdings of the Ra'athim were as rippled endings, heaving between times, with all fates leading to swallowed knives, murder as moaning, God's holy [censored]-erasure of wet death.
The King of Assassins presented to Vivec the Treasure Wood Sword.
'Milord,' the King of Assassins said. 'The prince of House Mora is now fond of you, as well. I placed him in the Corner of Dagon. His eyes I set into a fire prayer for the wicked. His mouth I stuffed with birds.' - http://www.uesp.net/wiki/Morrowind:36_Lessons_of_Vivec,_Sermon_22
There seems to be some sort of connection between Vivec himself and Morag Tong at least, other than that Mephala is Vivec's anticipation. In the Morag Tong headquarter they are using a regular altar as a shrine to Mephala, so perhaps they need to lie low and at least give a show of worshiping Vivec. I've always felt that Morag Tong was underdeveloped in the game though. Can't point out exactly why I feel that, but it seems a bit rushed and the NPCs seem to lack personality. Eno Hlaalu's dialogue is both unique and extensive of course, but he repeats himself a lot with ceremonial phrases so it all comes out as copy&paste work. Yes, I get the point with an assassin's guild being secretive, but when you advance to become Thinker, Knower and so on to Grandmaster one might think you'd have to know at least a bit about the guild you're working yourself through.