Hey Joe,
As of Version 3, of the ALEXA Firmware, you can now record 2 tracks of audio on board the camera.
While there is no quality loss to recording on board (PCM Audio) many people are still treating this camera very much like film. They are recording double system sound, and using the on-board track as a guide track for later conform, or just as a scratch track for dailies.
If however, you are recording in ProRes to the SxS cards, and just need one or two channels of audio (like an interview for example), there would be no problem with recording sound to the camera itself.
Cheers!
Suny