With release 2.01 of Google Apps Directory Sync you can exclude organizations within your Google Apps domain from being sychronized. This avoids having to individually exclude accounts like administrators or any other account that isn't in your LDAP or Active Directory.
Note also that there is an issue we confirmed with Google support that should be fixed in a future release where this exclusion rule will not work on any usernames that contain capital letters. So if the username is Username@yourdomain.com instead of firstname.lastname@example.org this exclusion rule won't work on that account. We had to use the GAM command line tool to rename some accounts to work around this issue for a customer.
If you would like some assistance with Google Apps Directory Sync feel free to contact Interlockit.com.