If you use the MSI files to install Folder Guard on the client computers, they also install the "Folder Guard" service that can be used to control the protection status on such computers:
PAUSE the service to pause the Folder Guard protection on the computer;
CONTINUE the service to resume the Folder Guard protection;
STOP the service to deactivate the Folder Guard protection.
Note that if you stop the service and deactivate the protection, the service itself is also removed, so you cannot start it after that! To reactivate the protection of such a computer, you need to redeploy the MSI package, using the GPO object.
Of course, if you don't want the users to control the protection by controlling the Folder Guard service, make sure they don't have the permission to control the services on their computers.