When the Web Adaptor is currently installed there is an option to disable or enable the Server Manager. However, there is no option to disable the REST Services Directory on the internet. To hide published service URLs on the internet, all services must be secured through ArcGIS Server Manager or the entire Services Directory must be disabled (both intranet and internet). I would love to see an option to disable it in the Web Adaptor like the Server Manager, but continue to be able to access it through port 6080.