If you just want to "turn off" the public facing part of a taxonomy (eg. just use it from grouping), you can do that when you [register it](http://codex.wordpress.org/Function_Reference/register_taxonomy).

Just set the `query_var` argument to `false` and WordPress will not recognize taxonomy page requests and simply 404.

    <?php
    add_action('init', 'wpse94193_register');
    function wpse94193_register()
    {
        register_taxonomy('your_taxonomy', 'your_post_type', array(
            // other stuff here...
            'query_var' => false,
        ));
    }

If you do need to allow logged in users to view the taxonomy pages (can't tell from the question), that's  different story.