Plen - several things:
Please read:
http://www.bmwmoa.org/forum/showthread.php?t=46055 - I've added that info to your thread title. It's important info as hexheads have had two different (completely different) brake systems. It's also useful for people who may be searching for this info in the future. Please do add this info to thread titles when posting in the tech sections.
On to your problem..
You mentioned you checked the brake light... did you do this by removing the bulbs and checking the operation of them? The hexhead is smart enough that if the brake light burns out, it will run the normal running light at 1/2 power, and only brighten it when you use the brake.. so it LOOKS like you have a brake light, even though the brake bulb could well be burned out.
To really check them - take the sockets out of the taillight and watch what happens when you turn the bike on, and then hit the brake.
Disconnecting the battery will do nothing if the fault remains. To do anything useful, a code-reader like the dealer has, or you can buy (GS-911) is really needed to determine why the system has turned on the warning light.
FWIW - some people have fixed the ABS/Brake-module by cleaning the electric motor on it.. it sounded as if in some cases the brushes in it may get dirty enough that they start to bind in the holders and don't make good contact with the amature. They also don't seem to fail all that often, so a good used one shouldn't be awfully hard to find, or too expensive.
Can we assume the semi-annual brake fluid flushes have been done (the clock starts when the bike is manufactured and should be done every two years from that date..)?