Jquery update module prevents removing js files on the theme level

Using a function like this

function phptemplate_preprocess_page(&$vars) {
  $scripts = drupal_add_js();
  unset($scripts['module']['sites/default/files/js/jquery-min.js']);
  unset($scripts['module']['js_file.js']);
  $vars['scripts'] = drupal_get_js('header', $scripts);  
}

to remove js files won't work when this module is enabled.