Is it possible to call a function but disable that functions hook calls?
You can't stop the hooks from being invoked unless you edit drupal_alter (or file_create_url) directly.

But you can use static vars to short circuit your own implementation so it only runs once for a given $uri:

function MYMODULE_file_url_alter(&amp;$uri) {
  $processed_uris = &amp;drupal_static(__FUNCTION__, array());

  if (!in_array($uri, $processed_uris)) {
    $processed_uris[] = $uri;

    // Even though this call will re-invoke the current function, the URI has been 
    // processed, so no infinite loop.
    $foo = file_create_url($uri);
  }
}