I'm not sure what will you do, but you can only do the following with someones cPanel username & password:
1. You can add blank index.html in directories without it, just so you can prevent smartasses from typing "site:blabla.com "Index Of" " on Google.
2. You can disallow Google crawling through some directories/files. Such as Admin Panel, and other files you don't wish others to see.
3. Blocking of unwanted country IP Subnets.
4. Chmodding files/directories, adding htaccess username & password protection for certain directories, or allowing only certain IP's to access some directory on the site.
Other than that, you can't do anything. If some CMS has vulnerabilities, you can't protect them, even if you do "protect" their site, some CMS's don't need writeable directories/files, aka they don't require anything to be uploaded, for example vBulletin, template is stored in the Database, and anyone can deface forum without having template files writeable, as its stored in the database.