configure your server to run PHP as specified user (for example use suexec + fastcgi). This way files created by PHP will have this user as owner and you can delete them with ftp client. Allowing everybody to delete (and update in fact) those files is rather security hole…
Almost every PHP web application that create local files faces this issue. Most open source PHP software that uses an ‘installator’ creates the config file through the http server with it’s permission and that could leave a security hole.
And sadly, most users totally ignore permissions setting them to something like 777 and they never try to learn the proper way. I would say you’re up against a problem that doesn’t have an easy solution. I would try to write a good instructions set and troubleshooting examples/stories.