I decided to just try ZmSetServerName at
http://wiki.zimbra.com/index.php?title=ZmSetServerName.
If you follow the directions exactly (stopping the services first), you get an error. If, instead, you just run the command, there is no error, and it stops the services automatically. That seems to have solved my "problem", or at least alleviated my fears. Since the internal DNS lists both domains fully, I'm not too worried about any leftover domain issues.