If it's CGI, then you're not going to have much luck changing this (as you've found).
I seem to remember someone having some PHP code that essentially reversed the effects of register_globals...
EDIT: Couldn't find it easily, so try creating a function such as:
function undo_register_globals() {
$lookin = array($_POST, $_GET, $_COOKIE, $_SERVER);
if(isset($_SESSION)) {
$lookin[] = $_SESSION;
}
foreach($lookin as $array) {
foreach($array as $key => $value) {
unset($GLOBALS[$key]);
}
}
}
and calling it at the very beginning of your PHP scripts.