I think bringing back a faction like that would really add to the atmosphere of Oblivion. We have the Office of Imperial Commerce in the IC Market District, but it's just a bland building where you can buy a rundown shack in the worst neighborhood of the Imperial City... not quite on par with a company that controlled all the import and export of Morrowind, owned (or at least controlled) a whole mining town and was rivaling or working together with some of the other factions in the game.
Adding a company like that would also allow you to give some explanations about where all the wares in the game come from. The company in Cyrodiil would have connections to the East Empire Company and other similar companies, making them the only legal importers of Ebony, Glass and Dwemer artifacts.