Truth is, Google doesn't care what open source project you want to make into GSoC, as long as someone likes your proposal, the project will get the $$ it needs :) Note Mercurial didn't make it to GSoC officially this year (probably have to go under PSF's name) - so even popular OSS doesn't automatically becomes a GSoC participant.
Tor wasn't just sponsored by the Navy, it was "originally designed, implemented, and deployed as a third-generation onion routing project of the U.S. Naval Research Laboratory." https://www.torproject.org/about/overview.html.en
When a company is recruited into a program like Prism, that doesn't necessarily happen through the CEO. Certainly, the company doesn't announce such a deal at an all-hands meeting, and omits it from their financial and regulatory filings.
The vast majority of a company's employees might be legitimately offended at the suggestion they are collaborating in such a program.
And yet, such a company can lose their customers and reputation, and may deserve that fate. It's a form of corruption. It's a hazard for customers. Those companies listed as participating in Prism have to bear the responsibility, whether or not most of the employees and even most of the company leadership can correctly claim to be victims.
Just kidding, turns out Google is not always evil. Good that HN gets a reminder once in a while.