I have tested this and can confirm that the following stops the "Call Waiting" BEEP on the SPA504G (FW 7.5.2) and SPA525G2 (FW 7.6.1). Can't comment on other models/FW.
set the call waiting tone 'ON' time to zero.... as this "440@-10;30(0/9.7/1)"
The format of this is "freq@volume;duration(on_time/off_time/freq_to_use)"
Just change the "on_time" to zero.....