Change autocomplete path with hook_form_alter()
On a stock installation of Drupal 7 and references 7.x-2.0-beta3 I was able to use the following form alter to successfully change the autocomplete path for a node reference field on the article content type:

function YOURMODULE_form_alter(&amp;$form, &amp;$form_state, $form_id) {
  if ($form_id == 'article_node_form') {
    $form['field_node_ref'][LANGUAGE_NONE][0]['nid']['#autocomplete_path'] = 'another/url';
  }
}


Another option is to ignore the form and use hook_menu_alter to change the callback for node_reference/autocomplete/%/%/%. Your callback should accept $entity_type, $bundle, $field_name which you can use to filter out which requests you want to respond to.