The dynamic between Varys and Littlefinger is even more apparent now that we know Littlefinger was secretly bankrupting the realm. Varys, as he was saying a lot in season 1 to Ned in the dungeons, is the "servant of the realm". His machinations are in service of the stability of the kingdom (if also at times self-serving, such as capturing the sorcerer who gelded him as a boy). Whereas Littlefinger only serves the realm by accident in pursuit of enriching himself, and as this season reveals has actively worked to screw the realm over badly (he could hardly be unaware of the consequences of borrowing so much money)