First off, don't put words in the anigbrowl's mouth.
Second off, it's not government hostility to investigate a bomb hoax that costs a lot of people money and inconveniences a ton of people. This guy wasn't engaging in civil disobedience.
Third off, the dude could have just walked to any of the dozen coffee shops in harvard square with free wifi and done this all in the clear, and been fine. Tor cannot and will never prevent traffic analysis if you're dumb enough to plug into the organization you're hoaxing's network. Tor created reasonable doubt, that's all it could do in this case, as a matter of physical limitations.
As I had said, it's a "hostile government" in the context of security analysis. Sorry, there just isn't a technical distinction between this kid and a dissident. To take a principled stand of saying dissidents should have the means to communicate freely, you also have to assert that you'd like for this kid to not get caught. Understandably this is a hard thing to do, given the chaos it would cause (is causing) in the short term.
On a technical level.. I don't see how Tor could have performed better here. It's physically impossible for them to mask the fact that this guy connected, through the harvard network, to the tor network. The rest of it is between the police and the guy. If they had gotten proof that it was his specific machine that sent the emails through some weakness in Tor, then I'd lay some blame with Tor.
I disagree that I have to root for this kid not to get caught. Tor didn't fall down, and I'm not rooting for Tor to fall down. He could have stonewalled the cops, or he could have taken the most basic precaution on earth of not doing it from his frickin dorm room, Tor or no
EDIT: Actually, maybe they'd be able to correlate his mac address if they subpoena'd whatever coffee shop the email came from. That's a much bigger fishing expedition for "any coffee shop that connected to a tor node that day", though. But anyways, my point is that Tor can't be held responsible for things it will physically never be able to mask.
Back to the technical, isn't this the point of Tor "bridges" ? Of course these don't work out of the box - they require finding out the address of one out-of-band and manually configuring it. Wider casual adoption of Tor would have also fixed the problem in this case (if the resulting Tor user list was too long to question everybody).
The whole point is that ending up on a shortlist means you are essentially caught. This kid may have gotten off by playing it cool. But translated into the dissident scenario, it's still a loss.
Given the proliferation of surveillance cameras, the coffee shop scenario becomes much harder. Assuming after-the-fact facial recognition is standard these days, it would only work if there were enough other Harvard students also on tape. Low latency is the mortal enemy of mix networks.
With time, I've come to the conclusion that the ability to (re*-create such tools is more important than any individual instance of such a tool.
I want to live in a world where the routine use is anonymous, with nyms only connected voluntarily. Of course people have to be smart enough to not post 'my name is XXX' in-band, but they shouldn't have to go to a distant coffee shop. If privacy takes work, that means it's only accessible to the few willing to put in that work, and will be viewed as an aberration by everyone else. It's only by making it easily accessible to everyone that it can become societally accepted.
To take a principled stand of saying dissidents should have the means to communicate freely, you also have to assert that you'd like for this kid to not get caught.
Realistically he would have been better off to call it in using a payphone (to the extent that he considered a hoax bomb threat a matter of necessity). I don't think you can automate away a complete disregard for security.
I'm guessing you don't even believe this to be a laudable goal, and that's precisely why we need anonymity tools.