well first of all take your site down.. not entirely, but for now add a simple index.html to your domain folder with a message that your site is temporarily down for maintainence. That way you wont lose any credit with your viewers.
2. These kind of scripts usually have a back door programmed into the system. so don’t try to manually erase that stuff. it will keep on coming back.
3. Got to CPanel and take a backup of the SQL database for the WP installation. Nuke the entire directory, except for the media files and make a new WP installation.
4. then simply go to the PHPMyAdmin and restore your original database in the new one. That way you wont lose any registered users, posts or comments. All you would have to do is install the plugins and the templates.