You could open the base unit and remove the speaker wire from the motherboard connector.
This would probably mean you don't hear the beep as the PC turns on but if its working fine then its not a problem.
If its like mine its just a small speaker like you would find in a personal radio. Just trace the wires back to the motherboard, touch a bare water pipe before touching the motherboard to get rid of any static electricity, make sure the PC is unplugged from the mains.