Undo to Taxonomy term system path unset with _menu_alter
The question is a little unclear, to reverse that effect, you would simply delete that hook_menu_alter snippet.

To change the paths to something else, you would use hook_menu and create the relevant menu callbacks.

The last step there would be to change the taxonomy_term entity_uri so it uses your new callback.

i.e redefine taxonomy_term_uri in hook_entity_info_alter

/**
 * Implements hook_entity_info_alter
 */
function mymodule_entity_info_alter(&amp;entity_info){
  $entity_info['taxonomy_term']['uri callback'] = 'mymodule_taxonomy_term_uri';
}

/** 
 * Custom taxonomy_term entity_uri callback
 */
function mymodule_taxonomy_term_uri($term){
  return array(
    'path' =&gt; 'mymodule/taxonomy/term/' . $term-&gt;tid,
  );
}


Not sure why you'd want to do that though ;)

edit: If you want to deny access, better to use hook_menu_alter to add your own access callback to the taxonomy menu paths. Alternatively, override the path with Panels or Views and set access control there.