It takes a standard action to stow and/or equip shield and only a minor to stow/draw a weapon, so by RAW you are better off putting away your weapon to drink a potion rather than your shield.
And actually, two handed weapon wielders are in a better postion for drinking - removing one hand from a weapon is a free action, and one can hold (but not wield) a two handed weapon with one hand. So, while you only have one hand on it you could only use it as an improvised weapon (and wouldn't benefit from such feats as Hafted Defence), but given that it is also a free action to drop the empty bottle and then a free action to return to your two handed grip, the character is unlikely to only have one hand on the weapon for long.