When you register your post type you can show/hide the UI in the arguments. I would approach it this way:
$allowed = current_user_can('administrator') ? true : false;
$args = array(
//other args
'show_ui' => $allowed
);
//register_post_type() function;
This will maintain the custom post type architecture while hiding the UI for those who are not administrators. For more information about WordPress User Capabilities see this page: http://codex.wordpress.org/Roles_and_Capabilities