No, that isn't the case; it is indeed the alcohol. The amount of co2 one inhales when drinking carbonated beverages is nothing your gas exchange system can't easily handle.
Hangovers are a result of greatly inhibited ADH production - anti diuretic hormone. Once this happens, your body thinks it is over hydrated and expels a lot more water than it should. This results in dehydration, and it further concentrates the toxins produced from alcohol metabolism.