I'm going to assume your talking about Corporate Edition for right now. You can change the behaviour by going to the SSC, All Tasks, Client Realtime Protection Options, and then uncheck the "Display Message on Infected Computer" setting.
For "regular" Norton Antivirus, I'm not sure, but I think there is a setting in there for suppressing the pop-ups, and then letting NAV take care of everything automagically?
J.R.