Bob Murphy's post, excerpting Glen Greenwald, summarizes my position very well. In short:

1) What Stack did meets the reasonable definition of terrorism: "deliberate use of violence against noncombatants to achieve political or social goals by inducing terror [in the opposing population]".

2) Most of what the government is classifying as terrorism, isn't. Fighting an invading army, no matter how unjust your cause may be, is not terrorism. Whetever injustice you may be committing does not additionally count as terrorism. Yet the label is being applied to insurgents.

3) It's in the government's interest, in taking over the terrorism label, that Stack not be called a terrorist, because he seems too (otherwise) normal. People want to think of terrorists as being "different"; a middle-aged, high-earning programmer ain't the image they have in mind, and if they did have that in mind, they'd be more resistant to make concessions in the name of fighting terrorism.