I wouldn't be surprised if the Twelve turned out to be the twelve followers who were with Venat when she sacrificed herself to summon Hydaelyn. I also wouldn't be too surprised to find out that they—like Elidibus, Emet-Selch, and Lahabrea—managed to avoid being sundered. The period between the world being sundered and the first rejoining is apparently called the Age of the Gods, after all, and it would make some degree of sense to call the Twelve gods given the disparity between a 1/14th person on the Source and an unsundered ancient.
Another thing to note about that era, apparently, is that humanity was sent back to the Stone Age in terms of technology and magic development. They only began to make up for lost time with the First Astral Era leading into the Second Umbral Era, respectively. I would actually like to know the source of this information, as I found it on one of the wikis:
Specifically, this timeline here. I feel like it vindicates my hypothesizing that Hydaelyn sundering the world necessarily lead to global societal collapse and so on.
tl;dr on that note: Hydaelyn may not be evil, but I'm almost certain she screwed up on a level that's... very hard to put into words. If she's at all self-aware, she probably has a very big guilt complex over it.