Two problems here.
(1) The article has nothing to do with Fukushima or TEPCO. It's about someone who sent anonymous death threats.
(2) Sherman and Mangano, the authors of the paper you linked to an article about, are kooks. Just google on their names together, and you'll find plenty of info discrediting their claims, e.g.: http://blogs.scientificamerican.com/observations/2011/12/20/researchers-trumpet-another-flawed-fukushima-death-study/
(3) The Open Journal of Pediatrics appears to be one of the many open-access journals these days that have no standards for publication. See http://www.nytimes.com/2013/04/08/health/for-scientists-an-exploding-world-of-pseudo-academia.html for more about these journals. I support the concept of open-access journals, but many of them are junk journals.
(4) Sherman and Mangano's junk science didn't get blocked by evil governments or evil corporations. They put it on the internet and nobody interfered with them.
In the 18th century, privacy was a pretty straightforward thing. That's why, in the 18th-century US, it was straightforward to write the 4th amendment. As a result, the government can't open my snail mail without a warrant, and can't come into my house and search it without a warrant.
The technological reality is very different in the 21st century. I support individuals' rights to use strong crypto and to control their own computer hardware and software. But it's undeniable that these rights carry collateral damage.
In 2012, the University of Pittsburgh was basically shut down for several months by a series of 145 bomb threats that were sent by email, anonymized via Mixmaster. This is not a good outcome.
If someone is using Tor to post death threats anonymously, that's not a good outcome.
Despite these bad outcomes, I still support the individual freedoms that let them happen. But that doesn't mean that it's not a real problem. It's very much like gun violence in the US. I support the 2nd amendement, but I recognize that that comes at a cost.
Yep, or consider the case of Pitt, which was basically shut down for several months in 2012 because of bomb threats: http://en.wikipedia.org/wiki/2012_University_of_Pittsburgh_bomb_threats
The worst outcome of this isn't necessarily that Boston got locked down, although that's definitely worth discussing.
The worst outcome is that lockdowns are becoming more and more common, far out of proportion to the actual risk. Once it becomes normal to lock down an entire city in response to a very real and significant threat, it then becomes much easier to feel normal about it when we lock down an entire college campus because a mentally ill homeless person made some faculty or staff uncomfortable. It becomes normal to do what some community colleges in my area are doing, which is to have an active shooter drill once a year in which adult college students are locked in a dark room for 30 minutes and told they can't leave. (This passive response is, BTW, not at all in line with what experts recommend in such a situation.)
Destroying 30 minutes of instruction for a whole campus and violating students' civil rights is way out of proportion to the risk of getting killed by an active shooter, which for a college student is on the order of 1 in 300,000 per year. A college student's risk of being a victim of rape, robbery, or assault is about 1 in 100 per year, but we're uncomfortable dealing with that -- in fact, there is a wave of lawsuits right now by women who say their rights were violated when their colleges refused to take action about their being raped.
To use an analogy suggested by Scheneier, active shooters and the marathon bombing are like shark attacks, and other violent crimes are like dog bites. The number of people killed by dogs every year is much, much greater than the number killed by sharks. But we find shark attacks much more psychologically compelling.
You are in a maze of little twisting passages, all different.