Did you ever solve your dilemma? I've think I've done what you are trying to do and can offer help if needed.
My setup is run by a controller made up of motorcycle relays, and the brake levers themselves trigger the brake light. Hijacking the brake signals should be easy on most bikes. You need 2 relays to do it properly; the first sends 12v power to the brake light, the second continues the 5v brake signal to the motor controller. The brake levers are the trigger for the first relay, the first relay is the trigger for the second relay. You'll likely need to do it this way too because they are sending different voltages to different places, and you need 12v to trigger the 2nd relay (on a motorcycle relays at least). It works flawlessly on my bike. The one caveat is that if I lose 12v power my brake levers no longer send a signal to my motor. I use a 12v converter with a lower voltage cutout than my motor to prevent this. The motor always dies before the lights do.
(Why motorcycles relays? They ARE a little bulky but also purpose built for exactly this. They are weatherproof, cheap and replaceable. My experience with circuit boards and outdoor weather has taught me the 2 don't mix well. For light riding you'll be okay but don't get caught in the rain unless they're sealed very well.)
