To change only JS, you do not need to hack the module at all. Instead, you can use the system to change which scripts are sent to the page.
template.php:
$scripts = drupal_add_js();
unset($scripts['module']['whatever/the/path/is/lightbox.js']);
$scripts['module']['new/js/path/lightbox.js'] = array('preprocess' => 1, 'cache' => 1);
$variables['scripts'] = drupal_get_js('header', $scripts);
js , .
, , Lightbox.