I put together almost the exact same setup for filtering my beer and wine. I use iodophor for my sterilizing agent. I mix up 2 gallons, put it in the first keg, hook up all the lines and set the CO2 pressure about 8 - 10 psi, and run that solution through the filter, into the recieving keg. I even let the CO2 bubble out at the end. I haven't lost much sanitizer in the process. The next time I might pull the first pint out before actually transferring to the keg, just to make sure there isn't a high concentration of sterilizer in the beer.
I really wanted it for filtering my wines, and with the short time in contact with the CO2, I'm not too worried about it carbing up. Besides, I let the wine sit for another 30 days anyway, before I bottle it.