This should not be nescessary as passing by reference is not required and ispconfig disables the warning automatically.
See /usr/local/ispconfig/interface/lib/app.inc.php Line 39:
@ini_set('error_reporting', E_ALL & ~E_NOTICE & ~E_DEPRECATED);
This works fine here with current PHP versions so my guess is that you have the ini_set function disabled in php.ini or something similar so that ISPConfig can not set the required error reporting level.
Either you enable ini_set in php.ini again so that ispconfig can set the error reporting level or you change the error_reporting in php.ini to:
error_reporting = E_ALL & ~E_NOTICE & ~E_DEPRECATED
and restart apache2.