PHP does not run as root unless your site is horribly misconfigured. It runs under the same user as the web server (because it is the web server that runs the code). Usually "httpd" or "apache" or "www".
I don't think you can get it to run under a completely different user. You could create another script, make it set-UID to another user, and run that from your PHP script. But keep in mind that if it is a shared host, everyone else will be able to do that too. So it's not very secure at all.
I don't understand why you can't delete the folder though. You realize it must be empty first, right? Also, you must have write access to the parent directory in order to delete (or create) the directory. That is, you you need write access to the directory that the file/directory is in, in order to delete the file/directory. You don't actually need write access to the file or directory itself, only the directory it is in.
