Simple Javascript to disable Drupal Overlay for admin_menu toolbar. Add to page with a hook_page_preproces.

gistfile1.js

(function ($) {

  // Don't use Overlay module for the admin menu (toolbar) links
  Drupal.admin.behaviors.overlay_exclude = function (context, settings, $adminMenu) {
    $adminMenu.not('.overlay-exclude-processed')
      .addClass('overlay-exclude-processed')
      .find('a').addClass('overlay-exclude');
  }

})(jQuery);