nukkui nailed this one head on:
Disabling perl is not the solution. I would hire a professional to secure your server.
You cannot just arbitrarily block or disable perl as you will indeed break Cpanel and can also mess up things in Apache as well.
There are many things that you can do to limit exploit potential, increase security, and control access but for items like this, I would not recommend inexperienced users attempting to tackle on their own.