"They say time is the fire in which we burn." Dr. Tolian Soran surely must have been thinking of the Bruma Mages Guild when he said that to Captain Picard. For the guildhall burns in the eternal fire for all time. Or, at least it did!
If you're like me, the ever-burning fires in the Bruma guild are an annoying consequence of the guild quest. I could see not doing something about rebuilding it immediately, but to just leave it sit? And with fires that never go out? That's silly. Upon teleporting in with a character who had already completed the quest line, I was reminded once more that I really REALLY wanted to do something about this. Now that I can, I have. The guildhall will undergo a staged reconstruction.
The first two stages happen on their own, with no intervention. The fires will be put out, and the damaged rubble later cleared. The last two stages will not proceed until asked for, either by you asking Traven about it or by you ordering the reconstruction yourself once you become Arch-Mage. You can keep track of the progress by checking with Raminus Polus. He will handle getting new furnishings in and hiring new recruits. You will not be required to pay for this yourself.
Due to technical issues involved in using the vanilla destroyed guild cell, the mod is forced to use a new cell for the rebuilding phases. All attempts to remove the noise left behind by the fires have failed. The only solution being to occupy a cell where those fires never existed OR to play a game with just this mod and Oblivion.esm loaded. Hardly ideal. Keep this in mind if you drop stuff in the burning hall, because you won't be able to retrieve it.