Ah. Perhaps I understand. (perhaps)
The createShortCut code is actually running on the client machine. It just happens to be in a document that has been generated from a .jsp that ran on the server. Here's what I understand for you need to do:
Put the file that you want to copy in a location on the web server that can be accessed through HTTP. Then in the script, you just need to copy the file
from its http://whatever location on the server. I don't know WMI stuff well enough (or, I guess WScript something different, right? that's about how well I know it, anyway) to know if it already provides a quick-n-easy way to do it, (like specifying a URL as the source location) but there certainly are ways to access HTTP from JavaScript. See
http://jibbering.com/2002/4/httprequest.html for some low-level examples. Perhaps look at
http://www.oreillynet.com/pub/a/javascript/synd/2002/08/30/mozillasoapapi.html which describes a SOAP API. (Although that's probably way too high-level.) Also, look at DHTML, which I've used to download documents within frames in the browser. There may be a simple way to insert the .ico into the browser's DOM, and then save it from there.
That's about all the help I can give.