To configure the cPanel MailScanner front-end so you can enable or disable it for individual cPanel user accounts, go to WHM > Plugins > ConfigServer MailScanner FE > Front-End Settings and set "Allow all cPanel accounts access to the front-end" to No. Click Save. Then go to Plugins > ConfigServer MailScanner FE > Enable/Disable Accounts (new button). Check the boxes for the accounts you want to give access to the MailScanner cPanel front-end, and click Change.
In versions of the MailScanner Front-end from v2.6 on, both disabled and enabled accounts are set to the default settings under ConfigServer MailScanner FE > Front-end Settings > Advanced Settings, including Default for spam scanning, default actions for high and low scoring spam, and default for virus scanning. So if you do not want accounts without the front-end to have any scanning at all, you should set the defaults accordingly.