CDNs will indeed mess with the results, but it would still likely be possible to tell the difference between a legitimate result and a forged one, especially if you know something about the CDN structures used by major site. And the more people run it, the more likely you can detect anomalies, much like Perspectives does for SSL.

SSL, incidentally, seems like a major help here: you could detect common DNS hijackings by accessing the site via SSL. If you access https://amazon.com/ , an ISP hijacking the site would produce either a certificate error or a connection failure (depending on whether they even attempt to listen for SSL traffic).