While it's easy for the viewer to predict the plot, it seems pretty unreasonable to expect Asuna to come up with the answer. That isn't really the first thing you would assume when someone says they can't play anymore.

Kirito only figured it out because he researches VR tech and had probably heard of Medicuboid before.
Additionally, he realized in the fight that she had most likely played VR games for as long, if not longer, than he had based on her reaction time and how well she could move in the game. Since she wasn't in SAO, there is really only one option at that point.