Daedra, dragons, various users of magic, and in fact many of the races, factions and entities of Nirn have experienced different facets the balance between power and restraint, sometimes with catastrophic results. The Dwemer represent only a single perspective that relates to this balance, namely the rejection of the divine for the pursuits of knowledge and reason. The lust for knowledge has dangers just as the lust for other forms of power and control. Additionally, the past abuses of power of any single group is not necessarily representative of all members of said group. In my opinion, bringing back the Dwemer in some form does not necessarily diminish the impact of the price their race as a whole paid for their hubris. I simply think that it could be done in a way that does not diminish the impact of the existing lore. Should the Dwemer return, the impact on the narrative would certainly need to be carefully considered, but I believe that Bethesda has proven that they are up to the challenge to make it work.
Seeing as the Dwemer are most likely nothing more then the skin of the Numidian now, it would certainly change quite a few things to bring them back...
The Dwemer are gone, they toyed with a God and failed... Harsh lessons are harsh sometimes.
As for the whole the Dwemer are uber thing, they are not. They were beaten by the Chimer during the war of the first council, before the Chimer became Dunmer and before the Tribunal became Gods... They can be beaten.