i had the same problem
there are few other threads addressing this issue..
this is what i did
"i hate the notification too. the default tone was loud and the caller could hear it as well.
i changed the ringtone by editing the registry. i am sure you could just delete the tone all together as well.
http://forum.ppcgeeks.com/showthread.php?t=41178
HKCU/ControlPanel/Sounds/InCallBuzz
I changed the Sound value from Notify.wma to Default.wma
So now it just beeps 3 times when a text comes in while on a call. "