I can see how they would use the Night Mother and Sithis though. The Empire would NEVER suspect the Dark Brotherhood to affiliated with Morag Tong, if they worship someone the MT would've had killed.... Just my opinion, but I think the Night Mother and Sithis are a ruse to hide the fact that they worship Mephala.
They're a secretive organization anyway, so they're hiding the fact that they worship Mephala from themselves?
Forgive me if I seem harsh, but your arguement doesn't pan out because you forgot something very important...the Dark Brotherhood itself is frowned upon. In fact, their existence breaks the laws of the Empire. They're supposed to be hunted and brought to justice.
Frowned upon? They aren't really. They're useful. They don't give a date I don't think, but the book on them says,
"In a remarkable syncroncity at a time when the Arena was a fractured land, the Morag Tong was outlawed throughout the continent. Every sovereign gave the cult's elimination his highest priority. Nothing more was officially heard of them for a hundred years. "
Then of course the organization is off the radar, and they reappear as the Dark Brotherhood in the second era.
"The important distinction between the Dark Brotherhood and the Morag Tong was that the Brotherhood was a business as much as a cult. Rulers and wealthy merchants now used the order as an assassin's guild. The Brotherhood gained the obvious benefits of a profitable enterprise, as well as the secondary benefit that no longer could rulers actively persecute them. They were needed. Even an extremely virtuous leader would be unwise to maltreat the Brotherhood."
We're in business! Then the Colovian Emperor Potentate Savirien-Chorak and every one of his heirs was murdered on one bloody night in Sun's Dawn in 430. We find out later that Savirien-Chorak was the son of Versidue-Shaie, making him at least 450 years old. Interesting to know the snakes can live so long. That is unless they like taking the names of previous rulers without adding numbers behind them, which is inconvenient.
Why would they give a [censored] about what the Empire thinks about them worhsipping Mephala when worshipping someone else wouldn't make a darn bit of difference?
The empire likes them for their secular nature. I think they have a don't ask don't care thing going on. Then again the officials of the empire could just summon Mephala themselves when they need a strike if the Brotherhood is too devoted, which means less money for the Brotherhood.
In my opinon, the only reason there are differences in Morrowind and Oblivion is because the dev team didn't do a good job panning out the DB in Oblivion. That's it. Plain and simple.
I'd say the same goes for the Tong and Brotherhood in Morrowind, to build upon your statement. The business of murder and murder accessories isn't something their team on MW and OB was much into I guess.