When I was reading the books I wondered if Varys was deliberately fomenting chaos in Westeros to aid the Whitewalkers. The defining moment in Varys life is when a follower of the fire god cut off his bits and burnt them as an offering, at the time I imagined he might be trying to aid ice versus fire as vengeance.
If that were the case weakening Dany (whom I can't stand in the TV show) would work to that end.
Except Varys has been consistent even in casual talk with tyrion who he shared his origin secrets with that his overall aim is to help the common people.
Wiping out life on the continent isn't a great plan for that.