If there's malware on your computer, it could just as easily keylog your password and one-time code the next time you try to log in to google, silently drop those packets on the floor (so you think there was just a connection issue), and then use your credentials to get access to your account.

If there's malware on your computer running as you, with access to things like USB devices, it becomes significantly harder (if not impossible) to do anything security critical on it.