There is currently no method for changing that option other than the VoiceAttack options window, no.
Assuming you still want other sounds and TTS actions to work, you can't just mute the entire application either.
If you have a blank (but valid) .wav file, you could use a batch file to copy it into the installation directory as "sys_on.wav" and "sys_off.wav", which will override the existing sounds, and being blank would produce no audible sound.
Otherwise a second installation may indeed be the simplest option