The only Imperial province with their own armies, religion, laws, etc. Probably the one that could inflict most damage on Cyrodiil in a war (they almost won the Four Score War, but Sotha Sil made a deal with the Daedra and could not get to Morrowind before Vivec suggested an Armistice).
Anyway, hopefully some help with the inconsistencies will help you create a good plot:
the Knights of the Nine are Cyrodiil's leading force, while the Knights of the Tribunal are Morrowind's leading force
The Knights of the Nine are a religious group, not a political force. They wouldn't interfere unless the Nine were opposed, which they probably wouldn't be unless Azura, Boethiah, or Mephala (who will probably come to rule Morrowind both spiritually and politically) decide to do anything - which they won't, as they are already more powerful than them.
The Tribunal is gone. House Redoran is gone. House Indoril is gone. The Nerevarine is gone. The Daedra can now claim the rewards of the investments they made three thousand five hundred years ago. No knight of the Tribunal ever existed, and now none ever will.
Standard Rules, but no Ebony or Daedric/Light Armor Variants
How can you have that rule when the former rock has been used in Dunmeri armies for thousands of years, and indeed is most abundant in Morrowind, and that Daedric is essentially the same thing, merely enchanted by Daedra, with whom the Dunmer are closely affiliated.
Tired of the lack of slavery?
House Dres will likely be bankrupted, yes. That will take the traditionalists from any considerable power, yes. But King Helseth is opposed by the tide of Dunmeri traditionalism itself; that will have no effect. He cannot enforce a law that the Dunmer people in its entirety defend as a civil liberty under the Armistice and according to their customs. Not in the face of the powers who have threatened him and the Tribunal since both came to any position of power, who now can take over Dunmer religion (perhaps the most powerful part of Morrowind's politics).
Knights of the Nine, are the official religion of the empire, if im correct, and Tiber Septim is a divine, so im assuming the knights of the nine would help out in this crisis, beating the heathens?
Daedra are more powerful than Aedra. The Nine Divines are Aedra, so they can only restore things to how they were, but Daedra can change.
And not many people follow the Nine Divines in other provinces as opposed to their own versions of them, or different pantheons entirely. They are a significant group, yes, but are still a minority. If the empire was to crumble to the point where Morrowind could declare war (which it probably has done), then they'd have no power to stop a war, or interfere in it.
The Tribunal are their religion, and they are defending their people.
I'll say it again; the Tribunal are gone. Now their lies are public and people will start to question why the Ghostfence has disappeared and the Tribunal still haven't been seen, the Daedra (who were always waiting for their chance to take revenge on the false gods - look at any Dunmer for evidence) and ancestor worship will come to dominate religion. If they aren't disregarded entirely by the new generation of Dunmer, then the Tribunal will be worshipped in the same way that Nerevar was under their rule. They definitely wouldn't be seen as gods.