SuHosin configuration for Drupal 7?
I imagine you could try and override the setting in a local 

php.ini

file.

For example.

/var/www/my-site/php.ini

disable_functions = system


Adding a single function instead of the list your host is using by default.

If that works, you could add other functions there, e.g

disable_functions = exec,shell_exec,popen,passthru,proc_open,system,pcntl_exec


Otherwise, you'll need to hack Drupal to remove those ini_set declarations and move them to the local php.ini file. ( not recommended )

You could also ask your webhost for help ( recommended )

Alternatively, find a new webhost.