Definitely a worry. But my impression is that implanted chips have a tiny, tiny range. this website (http://www.bsava.com/resources/microchipadvice/implantationsites/) gives veterinarians (heh - can't just say 'vets' in this discussion!) advice on how to scan animals for ID chips, and they talk about holding the scanner actually touching the fur, and making sure not to do it on top of a stainless steel table. So it seems ill-suited for figuring out where people are.

I guess my thought is that the employer who would use RFID tags in badges to track bathroom breaks is the same employer that would have the person whose desk is near the bathroom take notes without RFID. Like any technology, it can be abused, but it doesn't seem geared towards abuse -- at least in its current form. It could always change.