Try using the using the exec command.
It's like the system command and also only takes one parameter.
Your best chance of running anything as anyone other than the webuser is to create a seperate PHP script with your exec command in it.
So your one script would look lke this
<?
exec('init 6');
?>
Then in your other script use the PHP exectuable to run that script, like this:
exec ('/path/to/php /path/to/script');
To find the at to the PHP executable, type which php in command line. /path/to/script referes to the script containing the exec('iit 6') statement.