We have this problem with SPA504G's - and change the 'Call Waiting:' progress tone volume level.
Log onto the phone's web GUI with full 'Admin' and 'Advanced' rights.
Go to the 'Regional' tab, and at the top in the 'Call Progress Tone' section, you'll see an entry for 'Call Waiting Tone:'
We change this entry to ... 440@-30;30(.3/9.7/1) ... i.e. we change the tone volume from -10dB to -30dB which leaves it there but makes it a whole lot less intrusive! If that's too quiet, change it to -20 ...
We have included this change in the provisioning template for the phones for deployment on install ...
best regards
Graham Hill
Foxhall Solutions