Hmm, why not simply always use the recovery system but just not store the energy in the battery if it's full already (or capacity reached or whatever)?
Lets face it, some of the coolest parts of high power cars are dispersed excess energy, glowing brake discs or flaming exhausts and of course screaming engines.
ERS obviously can't store things when the battery is full, but if the issue here is the transition between ERS and traditional why not have ERS bypass the battery when it's full and dump energy in a radiator, ending up with the same result as traditional brakes (kinetic -> thermal) without having to switch braking system in the midst of braking?
If the ERS is full, you either switch over to dumping the heat into the brakes (no ERS, switching problems), or you start to drain the ERS to make room (no switching problems). Draining the ERS will give you the same thermal problem you have with no ERS, except you have the choice of not dumping it into the brake pads - you can have seperate external resistor coils, glowing and radiating.