To the best of my knowledge, the GBA mixes the PCM down to two channels (left and right) in software, as do any emulators for it. I've not seen any emulator or GSF player that can mute any individual notes before the GBA software mixes them down, so the best you can do is mute the left or right output channel.
edited 3:36 PM EST February 23, 2011
by tripskylark at 10:21 AM EST on February 23, 2011
As far as I'm aware, Sappy is strictly for converting to MIDI; as such, the only audio output from it is MIDI, with no emulated GBA output, so muting anything there would only get you less MIDI output and not serve the purpose you want. I might be wrong on this or the above, though, and am certainly open to being corrected if so.