saving JS settings in theme_settings.php file
I think you problem is this: drupal_add_js needs to be called at runtime. It's not some kind of registry function that adds your js file for every future page request. In other words, your code only adds the js when the form is being submitted.

Instead of calling drupal_add_js in your submit handler, store a variable using variable_set() to indicate that the js must be added. In your template.php file you can use the _preprocess_page function to retrieve the setting using variable_get() and call drupal_add_js if needed.