I thought at one point in time rubygems had a system in place to sign the contents of the gem? If not this might be an interesting addition. You could have a digest stored along side every gem file allowing you to validate the authenticity of the gem file... I'm sure others would have something to add to this idea...
If rubygems.org is keeping fingerprints of each gem, then it still isn't sufficient, since those could have been compromised as well. If there's no other trustworthy source of fingerprints, then maybe we need to crowdsource it. Built a tool that will md5sum all the .gem files in your local cache directory, so that we can look for any files that were changed on rubygems.org