I don't think Varis knows about that particular bit, since it's revealed pretty late in 3.0's storyline. However, this might be more useful in showing Varis' motivations:
You know as well as we what will ensue should these insatiable creatures be allowed to roam free--that their very existence threatens the life of this star. We but disagree on the solution to the problem.
Varis is entirely preoccupied with ending the primal threat, and he will not hesitate to exterminate anyone or anything that prevents him from meeting that goal.
edit: I don't know SE's Grand Plan, but based on Varis' behavior so far, it wouldn't surprise me if he threw in to help with the Ascians.