Which version of Exchange do you use? In Exchange 2007 you can use transport rules with multiple conditions to differentiate people from two different domains and apply the disclaimer accordingly.
Exchange 2007 Transport Rules - http://exchangeshare.wordpress.com/2008/05/17/exchange-2007-transport-rules-disclaimer/
Amit Tank | MVP - Exchange | MCITP:EMA MCSA:M | http://ExchangeShare.WordPress.com