I had a quick look around.   Couldn't find any instructions for Tomato, but found some for using Microsoft's ISA server to block it.  
http://support.microsoft.com/kb/925120/en-us
Basically, IF the tomato firewall offers filtering by User agent, then you can add the User Agent "MSN Messenger" to the list.
Having said that, I know of no router firewall that allows that level of blocking.