DeepZoom - cool. I've been wanting to play around with adding that but haven't yet found the time. If you end up with something that you think would be a good addition as a core GSP feature, consider sharing it.
Let me see if I understand the issue: You have two file types (.ismc and .xap) that are both text/xml and you want a different HTML template for each. Is that right?
Since browser templates are keyed off of MIME types, you will have to map each file type to a different MIME type (like you suggested). You may have to edit the IIS settings to map the new MIME type to whatever behavior is associated with text/xml.
Roger Martin
Creator and Lead Developer of Gallery Server Pro