You don't need to use Rhino to remove <script>
tags. Use simple CSS selectors in JSoup and remove the obtained nodes. Here a minimal example on www.google.com
public static void main(String[] args) throws MalformedURLException, IOException {
Document doc = Jsoup.parse(new URL("http://www.google.com"),5000);
Elements elems = doc.select("script");
for (Element elem : elems)
elem.remove();
System.out.println(doc);
}