Hopefully this is an ironic question, but the answer will be demography. Condor is near Arbroath, Kirknewton is on the west edge of Edinburgh so far easier for the majority of the population to reach.
Don't forget that thousands has been spent over the last few years on getting the Kirknewton site up to a standard where it can actually be used for flying operations. I think they sorted the airfield out just around the time that all gliding ceased!
Also, is RM Condor's future secure? There has been chatter about moving 45 Commando to Faslane but I'm not sure if that is still on the table.