I wouldn't worry about it since you're mixing a live session and this is an analog process. The limiting factor is the frequency response of the mixer channels. Just use lower frequencies in bwgen to create the difference frequencies.
Recording to disk requires sampling twice the highest frequency component of the input signal to get a decent reproduction and this is true of any digital audio so there is always some loss. Even if you convert a wav file to mp3 format, the reproduction of the binaural beat frequencies is still adequate.
If you have a spectrum analyzer handy, you can always check the degradation of the output signal frequencies.
[This message has been edited by shr33m (edited December 04, 2003).]