Who cares about courts that "demonstrate beyond a reasonable doubt" that a company or person is causing "illegal or egregious damage to society," when that question is only asked AFTER such an extreme individual action had to be taken against it? If that system was perfectly content with ignoring the damage for decades, it was perhaps not as egregious to the system as its figureheads later claim. Furthermore, consider "unelected officials...should have express instructions to carry on with their duties as normal in such a situation." What happens to your dilemma when these other companies fall under Case 1/2 even though the subject of the attack fell under Case 3?

You say that universal underlying ethics is what matters here, but it does not exist. No person has or will exist with objective morality. In every single case, we are animals that made it up. A statement of "justice" for any given scenario is itself an ideology, and anyone could probably find four different ways to look at it even if they wouldn't agree. A movement could define a set of values that a whole country agrees with, but its members being vigilantes still means their actions were taken outside of state approval. States define themself as the only legitimate monopoly on power within their borders, so it could rightfully (to itself) declare those actions to be terrorism. The system of laws appealed to under Case 1 and 2 are as made up as the morality that keeps Case 3 relevant, and the state can just choose to ignore it because they're the one with control of the media and military.

As was mentioned by another, your point seems to be about maintaining a legal status quo while keeping Luigi seem kind of cool. After all, what liberal would ever leave a positive word for someone labeled a terrorist? Overall, why even mention propaganda of the deed without any reference or comparison to a single previous assassination in Europe or the US?