Given my experience with ffmpeg I don't think it's possible, or there are workarounds I'm not aware of. I searched for the same stuff when I was using ffmpeg... without success.
Maybe you should try software like
GLC that works like FRAPS on linux, and only grabs the game output, not the cursor or another part of the desktop (also I feel it gets more FPS than ffmpeg).
Also there's VLC, it doesn't capture the mouse pointer by default.