Unfortunately it seems every linux user experiences a different problem with the game. The game is still in development and linux support is fairly primitive. Eventually, I'll get the OpenAL code working in Linux. Perhaps that will work out better. I'm also considering switching to an sdl base, but ironically the sound in the quake2 sdl port does not work for me.
I'm not sure why the sound is so choppy for you or if it's related to the sound init code displaying 11khz. I'll have to take a look at it on my system and see if it also runs at 11khz. I'm running Debian and the sound and mouse movement work properly. What did you change to get the mouse working on systems w/o dga?
Also, how often do you release CD's? As I mentioned, this game is still a work in progress, so there will be continual updates for a while.