Not too long ago I started a thread asking for something similar. At the end of the Great House Dagoth mod, Vvardenfell isn't "blown up" (even if you completely side with Dagoth Ur) since that is the somewhat "kinder and gentler" of the Sixth House mods. Anyway, my character is the new "God-Queen" of Morrowind, yet the Imperial Legion guards still tell her to "keep moving" and "move along". That is of course a huge no-no.
They shouldn't even be there since she and Dagoth Ur have taken over.
Since then I have been trying my hand at modding to shape the game-world as it should be with the GHD ending that I chose but since I'm not an expert when it comes to modding, it's been a long, slow process. So far all I've gotten around to changing is making adjustments to the Imperial forts, placing Sixth House banners all of the place and replacing the Legion guards with Dreamer Warriors. I'm also having Dagoth Araynys and his servants move into the Caldera governer's mansion.
So anyway, yes it would be nice if there were mods out there for those of us who play characters that have "taken over".