You should be able to overwrite it with another file of the same name. Just create or find a small .wav file and name it phoneon.wav. Then copy to \Windows.
Edit: I looked and found this reg entry. I assume that you could change the Enabled to 0. If not, change the file names.
Code:
[HKEY_CURRENT_USER\ControlPanel\PhoneExtendFunction\CDMA\FlightModeOnOFF]
"Sound_off"="\\windows\\PhoneOff.wav"
"Sound_on"="\\windows\\PhoneOn.wav"
"EnableSound"=dword:00000001