This is browser behaviour that Alfresco has very little control over, beyond ensuring that the file is streamed to the browser with the correct MIME type (which is the case for Excel - that's the setting you commented out in the web.xml file).
All I can suggest is to check your browser settings and make sure your browser is configured to open files with MIME type "application/vnd.ms-excel" with the Excel desktop application, or at the very least to prompt you and ask what you'd like to do with the file.
Cheers,
Peter