This is going to be a terribly unpopular point of view I'm sure, but all specific details of his particular case aside ... what is an individual or small business with limited resources going to do if they end up stuck in an IRS quagmire? Is the IRS really defensible at all here?
What happened is exactly what can be expected to happen when the rules of the social contract are violated. For social contracts to work, there must be a way for parties to peacefully resolve arguments. In the case of the IRS (in particular), you have a complex, constantly changing system, with little recourse for resolving disagreements.
I've been really poor, and it's easy in that situation to adopt an us versus them, self-defeating attitude towards government and bureaucracy. Resolving any disputes requires resources, and when you don't have those resources, you find yourself struggling on the losing end of deals over and over again.
There are, at least, thousands of people that would imagine themselves doing what Stack did, and for much the same reasons. Doesn't that practically require that the tax system get reviewed, and fixed?