This is exactly what the problem is for many people. They complain that they don't think she's actually a "master of The Game", but then complain that she constantly bests them and they can't out-maneuver her. To me, it really just comes down to the fact that it's really difficult to best her.
Here's the thing through, when your having those early on arguments with her about magic and the need for the Circle I could understand/accept how she can intellectually outmaneuver through solid, well-thought out arguments. That's fine for the most part with a couple of exceptions, but in those arguments she's not acting as a player of the Game, but as someone whose just having an argument with another person. There's none of the veiled threats, political loopholes or mind games that are associated with the Game in those conversations.
When you get her disapproval scene though she is trying to use the Game against you to get her away. Unfortunately, that scene makes the Inquisitor and Vivienne look stupid for no reason. Vivienne just lays out her complaints against you and moves your furniture and for some reason that forces the Inquisitor to just shake her/his head and walk away.
She doesn't threaten you with blackmail, she doesn't tell you how much you need her for Inquisition to succeed and she doesn't try to convince you diplomatically that your going about things all wrong. She doesn't use social mechanics to control you in this instance at all. Therefore, there's no reason for you to not flat out kick her out of the Inquisition or reprimand her. Sera can get mad you and start insulting to your face and the game allows to kick her out for it. Vivienne does the same thing but in a passive-aggressive manner and you can't do same to her for some reason. It's odd and to be honest that furniture scene should have ended up with Vivienne leaving of her own volition or with you kicking her out yourself.
The point is Vivienne doesn't actually manage to outsmart you in that scene, she just manages to get away with being an insubordinate ass for no reason. That's not her being a master of the Game, that's the game itself not allowing to punish her for no reason.