Could you just use GPO to specify who has what rights to the messenger service. You can even specify the startup mode. You can also give a user permissions to Stop a service, but not Start it.
Here is what I would do if I were you. Note, your clients must all be 2000/xp for this to work.
Edit/Create a GPO in the container that has all your Computers. Go into "Computer Configuration", "Windows Settings", "Security Settings", "System Services". Then Find the Messenger service. Check the Define checkbox, This will then bring up a Security Box. Give "everyone" only Read Permissions, then add administrators and give them full contol. Say OK, then set the Startup Mode to Disabled. Now after GP replicates it will set the startup for the messenger service to disabled on all the computers. The messenger service will still be running however, you will have to stop it, or reboot the computers.
You could also do it the other way and create that login scrip to do a "net stop Messenger". In that case, when you set your permissions on the Messenger service, click "Advanced". You can then set to allow "Stop" Permissions.
Hope This Helps!
Dan