Last week Google updated their verification process for Webmaster Tools. A known issue was that it broke the ability for Google Sites to verify in Webmaster Tools. Yesterday, Google resolved the issue and now Google Sites can be verified without an issue.
An updated Google Webmaster Help thread there are a couple webmasters who have confirmed it is now working.
I personally thought it would take longer than a week to fix, but I was wrong and glad I am wrong about this one.
Forum discussion continued at Google Webmaster Help.