Use PHP5. The INI for that has them off by default.
Or you can install your own version of PHP
OR you can use PHP4, Apache mod, which will give you access to use "php_flag register_globals off" in your .htaccess file.
Those are the only options you have to turning them off. Pick one.
I'd recommend using PHP5.
Issue is that the location of the INI file is hard coded into the binary of PHP. The only way to override that (as CGI) is to recompile PHP. You CAN change it for CLI, but not as CGI.