ISPConfig allows you to add any apache directive you want to a vhost, we are running several drupal installations on ISPCOnfig, e.g. howtoforge
Just add the directives you need to the apache directives window of the website. If you use directives that need special apache modules, make sure that you have loaded the modules in your httpd configuration file before.
If you want to use apache directives in .htaccess files, make sure that the directives are allowed fo use in .htaccess files in your apache configuration (AllowOverride setting for the directory /var/www/*/web).