What about using a 3 way solenoid like this one?
http://www.wicvalve.com/3-8-3-Way-2-...?categoryId=-1
(3/8" 3 Way 2 position Air Directional Control Solenoid Valve)
I'm thinking you would basically plumb it backwards:
"A" (Outlet) = line in from the CO2 Scrubber
"P" (Supply) = line out to the skimmer
"R" (Exhaust) = open / room air
When the solenoid valve is closed, the skimmer would pull air into Port A (from the scrubber) and out of Port P (to the skimmer). When the valve is open, the skimmer would pull air into the Port R (open port / room air).
As long as the solenoid does not require either positive or negative air pressure to operate, would this work?