You never say what the circuit breaker ratings are. What amperage are they supposed to open?
I think I would ditch the circuit breakers and replace them with an ATO style fuse. You can get a nice in-line ATO fuse holder from Digi-key:
http://search.digikey.com/scripts/Dk...&name=F1086-ND
Put a 20A fuse inline to each fan and be done with it.
You are correct about the powered-off fan; a free-wheeling DC motor is a generator.