If you write a script that does:

1.) stop all services that were started as StartupServices, ie/ run 'SystemStarter stop'

2.) stop all services that were started outside of StartupServices (like something that was put manually into rc )

3.) if you are allowing remote ssh logins, warn users that the machine is shutting down with "write"

Run the script as root and then do the shutdown. Or write an AppleScript that does the shutdown for you and add that to the script.