Wow. If I understood it right, I think a lot of what I'd thought is true. For instance
Spoiler:
The disease or "Hinamizawa Syndrome" was discovered recently, probably during the dam incident, since vaccination and exposure are only now near completion.
The government recognizes its legitimate danger above and beyond any modern epidemic, since there are no symptoms and death is not given, unless the person is agitated, and the patient will not die alone. How does one quarantine a disease when there's no way to tell if a person has it, or if they had it and overcame it, and testing treatments brings with it the risk of creating a psychopathic killer? Each year creates more tension, straining the situation further. Thus the government has set up a two-tier plan, first to try to cure the disease, and second, in the worst case, to eradicate the disease along with its hosts and environment. The Yamainu and 34, for some reason, want to expose the situation and the government's tactics by making things as messy as possible. The SDF probably were required to kill the population, but to make sure that everyone seems to have died from a natural disaster so the government isn't questioned. The Yamainu are probably the ones that chased people and killed them in the woods, since the SDF would not stop until they'd found and eliminated the bodies and evidence instead of leaving traces of foul play behind.
As for why the vaccine hadn't been widely distributed, I think that would have been dangerous in this case. You'd basically be telling the people that they were sick and didn't know it, and that the right amount of tension could make any one of them snap and butcher their friends. Not only would many people protest and resist in disbelief, but belief would mean suddenly discovering that everyone you know could be a killer with you high on their list. Basically, if anyone knew what was really going on, the result could very well decay into an absolute bloodbath. The government can't openly pursue treatment, but if they don't go fast they'll have to take measures that go far beyond any form of taboo. It would be far too easy afterwards to paint the government as an evil that must be destroyed. No telling how far you could ride that wave.