Why you don’t create a service (A) that does all these tasks, and then create a client (B) that invokes this service?
For the tasks that A would have to perform (stop/disable Schedulers, File Polling, Packages, Adapters, etc ), you can find the related services at the WmPublic folder (Schedulers, Packages), WmART (adapters). For the file polling notifications, you can peek around the DSP pages to find out which are the services the DSP calls to enable/disable the file polling notifications.
To create the client B, the wm Developer tool can create such client for you: open the service (A), then access the menu | Tools | Generate Code then choose the flavor you want (Java .NET, or even C).
You could try creating a service which handles an FTP request. Include all of the IS related commands in this service. You could then invoke this service from a dos command by issuing an FTP request to the service.