I think a little carbonation is always beneficial to a cider, just make sure that you kick up a little bit of the yeast while transferring it into the bottling bucket. It may take an unusually long time (4+ weeks) to carbonate properly, but it will.
After aging the cider for 6 months, the vast majority of the CO2 trapped in the solution from fermentation should have dissipated. If you're still a little bit uneasy about it then you can go to your LHBS and buy a "wine saver". It's a vacuum pump that's used for pumping the air out of an uncorked bottle of wine. If you stuff a carboy bung into the receiving end of the wine saver and use it to create a vacuum inside of the carboy then the CO2 will come out of the solution.