The eye of Mangus is not in Skyrim anymore, and it's doubtful that it would have the power to destroy an entire race at once. There is just one thing that's powerful enough to do that. The Heart of Lorkhan, now even assuming the Heart is in Skyrim which I find unlikely, then they would still need the profane tools to manipulate it.
And we know that they don't have all three of those things, the likelyhood of them actually manipulating the heart in another way is incredibly small. Not to mention that the study required for something like that would take a great many years with access to the heart.
I'm not considering the Heart is in their sight or desires. I believe something equal, although unknown to most, is nearly within their grasp.
On what this is exactly- I would not know. Although it could be possible this object-artifact would owe it's origins from the dragon ruled era.
The era to which is relatively still has enough unknowns and confusion for an artifact of power to be left obscured within the history books.
Or like the Heart of Lorkhan and the dwemer, the thalmor simply stumbled upon something new. Some undisturbed piece of an aedra.
To the matter of them having the knowledge to manipulate such an artifact. Well going off the speculation that the thalmor already have foreknowledge of it,
the possibility of them already being within sight and study of it is high. What would be unknown is for how long. So when did the thalmor start
their small occupation in Skyrim? was it after the Markarth incident? if we took their occupation as a starting point and compared it to the current date,
then one might have something to go off. Comparing this to the length of time the dwemer took to study the heart of lorkhan would be reasonable.
If everything looks to check out then I don't see it as a problem for it to be a possibility in a dlc.