Actually they appear to be caching the pages, which is how they are able to detect what is highlighted (otherwise it would be cross domain scripting). So they could just have their caching script strip out that JS and problem solved.
I image that page caching could lead to problems with some sites though. I wanted to do something similar for a project I was working on but scrapped the idea because I couldn't get around the whole cross domain scripting issue, and caching just introduces a host of other problems.
Awesome Highlighter uses frames to view other websites and some websites prevent their pages to be viewed in someone else's frameset (if (top != self) top.location.href = 'example.com'). There is no way I know of to disable this and need to respect their wish not be viewed in frameset.