You can use the same php.ini for all your sites, and just override certain bits of config for some sites.
This is done in httpd.conf inside <virtualhost> elements.
Look up the php_flag, php_value and php_admin_flag and php_admin_value commands here
In the manual
These are for httpd.conf not php itself.
It is not clear whether you can set up disable_function in this way - the manual suggests maybe no - but you can still try it.
Mark