RTMP authentication is handled in a separate AddOn package. It is here:
http://community.wowza.com/t/-/45
We currently do not have a way to extend this system to provide custom methods of authentication. The current system uses a username/password lookup in a flat file. I will consider extending this support hooks for plugin in other methods but for now it will stay this way.
The RTSP/RTP mechanism is more extensible. Again, it take a little work but it can be customized.
Charlie