Since I disable functions that ispconfig needs to run properly it becomes unusable. There is a way to have a custom php.ini for ispconfig:
place your custom php.ini settings in /etc/php5/cgi/php.ispconfig.ini
add -c /etc/php5/cgi/php.ispconfig.ini to exec /usr/bin/php-cgi so it looks like this:
exec /usr/bin/php-cgi -c /etc/php5/cgi/php.ispconfig.ini -d magic_quotes_gpc=off -d session.save_path=/usr/local/ispconfig/server/temp
Will the custom changes be overwritten? Is there a better/safer way to do this?