Registering of a Partner Service is nothing but adding an entry into the CATALOGENTRY table. This is done through the API addEntry() in the CentralCatalog Class. So removing the entry from this class should unregister it. However there are no Remove API given for it
So I think if you can put a HQL query to delete the entry from the DB directly, it should unregister the partner service.
I haven't tried that yet though. Just a pointer.