100% protection not possible but you can harden the config
for example:
1. Disable root
2. Using SSH key instead of password
3. Change SSH port
4. Open SSH port only from a particular IP
There are may ways to harden your server security
shared whmcs!!??
Strange.. Maybe OP saying many providers giving WHMCS as a value added service/addon with their shered hosting..
However these addons are paid as it's no way possible to give free licenses