If your hosting company is blaming a configure.php file when the real culprit is the fact that the server's apache and/or vhost is improperly configured, then you might want to reconsider whether that hosting company is competent enough to manage your site.

Your domain's vhost needs to have index.php added to the DirectoryIndex directive.
If your host isn't competent enough to do that for you for all your domains, then you'll need to do it by hand yourself by adding a public_html/.htaccess file and add the directive there yourself.
But I strongly suggest that you should NOT need to do it yourself, and that this is a sign of further problems to be anticipated down the road.