One way to delete users en masse from an ArcGIS Server site that uses the ArcGIS Server identity store is to access the machine the server is installed on - from here, go to \config-store\security\users. Select the users that need removal/deletion from the site.
I know this is not at all an elegant solution, but it is quick and easy, and seemingly accomplishes what I need with out any adverse side effects. I'd be curious if anyone from esri or otherwise could come up with a reason why exactly this might be an ill-advised hack other than it not being good practice to modify anything manually in the config store of an arcgis server?