Mark the domain as deleted by running the commadmin domain delete command. (See the Chapter 5, Command Line Utilities, in Sun Java System Delegated Administrator 6.4 Administration Guide).
Remove services from the users of that domain.
A service can be a mailbox or a calendar. For Messaging Server, the program is called msuserpurge. (See msuserpurge in Sun Java System Messaging Server 6.3 Administration Reference. For calendar services, the program is csclean. (See Sun Java System Calendar Server Administration Guide.)