thanks for asking.

The Apple Remote is a special case in that Remote Buddy has to offer 
a way to temporarily give other applications access to it.

So, in short:

- deactivating the Apple Remote in the RB menu will deactivate RB's 
AR driver, thus the system falls back to the software shipped by 
Apple (=> a press on Menu invokes Front Row).

- deactivating the Built-in IR sensor entry in the RB menu will not 
deactivate RB's AR driver (RB keeps complete control of it), but RB 
will ignore any events it receives from the AR while the receiver is 
deactivated. And this is also the functionality you're looking for 
(please correct me if I'm wrong).

Also, you're right in that the MacBook waking up in response to IR 
commands is a hardware (or AppleIRController.kext) feature and - as 
far as I can tell - can't be turned off.

Best regards, 
Felix