Since InstantCommons loads resources from the commons, a more accurate way to find a list of wiki's using it would be to parse the commons access logs for wikis. It would be a more complete and comprehensive list of public and private wikis using commons, and would make this list redundant.
Topic on Talk:Sites using InstantCommons
It wouldn't be very nice though. Some private wikis may not want to be listed simply because they implemented InstantCommons.
Simple matter to make an easy way to add a site to a blocklist not to display.
That is an interesting idea for another reason: if MediaWiki, or Wikimedia, could identify every wiki which uses Commons images then they could be notified if there is an important update to Commons (like the one earlier this month changing http to https, which made all images vanish), though that might depend on whether contact details were displayed.
Another possibility would be to notify an outside wiki if an image it uses is renamed or deleted, though if that means trawling through every wiki whenever any image has changed, just to see if that image is used, that would be so frequent and intrusive as to have potentially the same effect as a DDOS attack!