RE: Stopping Sametime on Domino Ben Williams 25.Mar.14 02:36 PM Lotus Notes Administration 8.5.2 IFR1Windows
On Windows I have always stopped Domino using the service (if configured) and I have been supporting it for years and on many customer environments. During shutdown the various Sametime related services stop first and it's written to Domino that the service has terminated and then Domino continues on it's merry way shutting down adminp etc etc. The main thing to avoid is telling Domino to restart as this could (though I have never tried nor been bothered) restart Domino before Sametime has terminated.
I haven't seen that recommendation though that's not to say it's not there.
If you're worried then just stop the Sametime Server Windows service and then stop the Domino service. I'm sure you could write some batch file or powershell script to do that.