Configuration for Application Protection is missing in SGAC under Administration -> Threat Protection.
"Application Protection" can be configured using CLI.
CLI commands can be use to configure application protection.
Blue Coat SG-VA Series#(config)application-protection
Blue Coat SG-VA Series#(config application-protection)?
disable Disable the application protection service
download Configure download parameters
enable Enable the application protection service
exit Return to (config) prompt
no Reset a parameter
view View the current settings