Incompatibility with theme_menu_tree() in theme layer

We've experienced an issue where using theme_menu_tree() in the theme layer changes the admin modules's menu's to the point they don't work properly.

As admin is dependant on the default theme_menu_tree() implementation, our solution was to override theme_admin_menu_tree_output() in our theme layer and customise the last call to theme_menu_tree().

function MYMODULE_admin_menu_tree_output() {
        ...
	/* stop it from using our new menu tree and use Drupal default */
        //return $output ? theme('menu_tree', $output) : '';

	if($output) {
		return '<ul class="menu">'. $output .'</ul>';
	}
}

A better solution may be to hardcode this into the Admin modules theme.inc, or create a new theme hook just for that call??