What about us poor admins who use it for legitit. purposes.... "File server is coming down in 10 minutes, save all open documents NOW!"
Well, I think the best you can do if you actually want to use the Messenger Service for its intended purpose is block the ports at the router / firewall level.

At least that way you won't get the pop-up spam on the Messenger Service but you can still get messages from your network monitoring software and your printers and net send messages to your users.