I didn't quite follow your description of the application, i.e. the relationship of Java and JavaScript (some on the server in JSP; some on the page as well?). A general answer for future reference is that if you have JavaScript on a page, you can reduce the page size by moving the script into an external file and including it on the page with <script src="URL_to_script.js"> <script> tags. You also benefit from the greater efficiency of using the browser cache for static files like script.

There are all sorts of security restrictions on JavaScript in the browser. Doing things to the window, like closing, resizing, or minimizing, are usually restricted, though some browsers let it happen with a dialog box asking the user's permission; that's a pretty obnoxious disincentive to even try. Since not all browsers support those features in script, they're rarely used except in situations where you control the browser--e.g. corporate intranets.