You could do it the other way - *-ScriptMap aspnet_isapi.dll so that all requests are seen by the asp.net pipeline and can be handled by your handler, and the ones you do not want can be returned back to IIS using the DefaultHttpHandler mechanism - no ISAPI filter needed. Disadvantage would be that there would be performance degradation for stuff that you wanted IIS to handle anyway.
If you want to stick with the current way - you can look up the physical path of the url yourselves from the metabase.