You're right. The bit about 'absolute certainty' was hyperbolic on my part. How about this though;

You think it's too much to ask for the FBI to be able to stand up and say that this particular threat of violence, which feels like little more than chest-pounding script kiddies, is not credible?

My initial reaction was the physical threat was little more than a joke. The FBI and Homeland Security do need to be able to give proper guidance on credible and non-credible threats, and I think in this case in particular, it's a good example of something which I really would have hoped they could have explicitly labeled as non-credible.

Or to state it another way, if the accepted reaction is that we actually have to treat threats like this as credible, if attackers start spamming these threats are we just supposed to shut it all down?

What companies are looking for is a liability shield, and a public reassurance that they can use as a backstop for disregarding the threat. Otherwise they have no choice but to cave-in. So I think we depend on the FBI in specifically these cases to provide that level of assurance.

I somewhat feel for many of the theater owners in this case. After the Dark Knight, some tried to sue the theater because they "didn't prevent it" from happening, so something like that. The theater's defense was that they had no prior knowledge. With our litigious nature here in the US, having a vague threat that the theater might be attacked, they could lose that defense.

I agree with your premise though: there is no possible way for society to have absolute certainty of the validity of something so vague as the threats issued. To cave to those demands is absurd.

(full disclosure: I work for a company that owns a large number of theater screens, though not within that department. These are my personal views.)