Sometimes the notifications are more important than what's going on on the screen, and most of the times I would prefer not to miss out on incoming messages...
This option shouldn't be anoying, IF you make a simple button to turn it on/off, just like Home, Back, etc.... OR
If that's isn't an option for you guys... you could also implement it like Windows Media Player did... and place the option in the filemenu
As long as it can be turned on and off there shouldn't be any problem