So I looked into this since I could not remember the way to remove a mailbox and not the user account.  From the Exchange Management Console starting with Exchange 2007 (had to test this as well), if you select Remove on a mailbox, it deletes both the mailbox and the user account.  To remove just the mailbox and maintain the user account you should select Disable.  This will disconnect the mailbox from the user account.  The disconnected mailbox will then be purged after the retention period or you can force the removal manually.