The AppleScript for this is pretty simple:
tell application "iTunes" to stop
You can make this easily accessible by creating a Service.
Open Automator and create a new document. Select the Service document type. Set the Service receives: menu to
no input. Drag in a
Run AppleScript module and paste that code into its text box. Save the service and give it a name.
You'll now be able to activate it by going to the current app's menu and choosing Services-> Stop iTunes (or whatever you named the service).
You can assign a keyboard shortcut by going to System Preferences-> Keyboard-> Services, finding the service (it should be under General at the bottom) and adding a shortcut.