The way that the server side redirect works is to listed for the page being submitted, then do the processing and finally go to the page specified. It sounds like it it going to your index page. The server side code does not know of or care about the state of the page, so even though it is in a popup layer, the redirect will still occur within this open window.
What I was suggesting here is that you set this redirect page to a special page that you have crafted that just has the js on it that will close the window. This would give you the effect of having the window popup, then after the form was submitted and the server side processing is completed the redirect would occur. If the only thing on this page was some js to close the window you would just see it disappear after the user submits the form.