Yes you can (except upon rebooting).
The reason the services are started or restarted automatically is because of the bl_cpanel hooks. To disable them, run this command:
/usr/local/cpanel/bin/manage_hooks del script /etc/betterlinux/cpanel/bl-cphooks
Then stop the services you don't want to run. If you want to stop CloakFS and cpud, for example, do this:
service cpud stop
service cloakfs stop
With the bl-cphooks disabled, no BetterLinux services will auto restart. The only exception will be when the server is rebooted.