Not sure if Kerry still held the copyright to his book. A common practice is for the author to transfer his copyright to his publisher as part of a the author-publisher contract.
As for the HRC thesis, my guess would be that Wellesley held the copyright and finally agreed to waive it (perhaps for a fee). A lot of private colleges are in poor financial shape these days.
Most thesis’s are held by the school, and are often public domain. At least most of the ones I dealt with at Iowa State were.
I don’t know if it was Kerry’s book, but it was a published book, and somebody owned the publication rights. If a person owns the rights to a book, and doesn’t want to sell it for less than $100 bucks, that doesn’t mean we can scan it onto the internet and distribute it for free.
Since the site was taken down, I’m presuming the copyright holder did not set it up to allow access to the book. Just someone trying to provide information, but doing so in the wrong way.
Why would Wellesley have the copyright? It's Hillary's unless she specifically assigned, in writing, all copyrights to the College and I've never heard of that.