You know I played Morrowind for 8 years, and never knew killing Aryon was apart of the Mages Guild questline. Damn, there's still so many things to discover in that game, after all these years.

Morag Tong and Mages Guild simply have one more quest after MQ is finished.
If Trebonius is alive and you finished his Dwemer quest, he will ask you to kill all the Telvanni Masters in Vvardenfel. Since I always kill that imbecile, I can't even get it

(nor would I do it... not to mention that in Rise of House Telvanni mod I ordered Mages Guild annihilated, save the Argonian and Edwina)
Its only a part of the questline if you choose to follow mad Trebonius to the end.
The thing is, all quests in TES are canonized and thus completed by someone.
Either way, nobody says that the Telvanni lords will be from TES3. The towers in TES3 are just new colonies, most Telvanni wizard lords lived on the mainland and in Port Telvannis.
Granted, I hope it is Fyr...
Killing him was bad..very bad.At least thats what the popup insinuated in very vague terms like"You have altered the thread of fate do you wish to continue in this world you have just royally jacked over?"
You get that message whenever you kill a character who is part of MQ... no matter how important or unimportant he is.
Had to make this image when I read that!
http://i47.tinypic.com/zipxe8.jpg
Love this thread, its awesome.
looool XD