I see what you're getting at with civil disobedience though... I suppose the difference is in scope and scale.
Someone passively resisting a bad law can certainly be said to not be a vigilante; they're not actively trying to to bring about their desired brand of justice, they are simply refusing to comply with the current legal version of it.
One would not expect to bring out change only by themselves via civil disobedience, it's power comes from being applied across a group of people. Vigilante justice is different; you simply fix whatever situation is unjust.
If Aaron had simply complied with his own manifesto (e.g. downloading an article at a time, organizing others to download articles, etc.) I think we could safely say he was simply being civilly disobedient.
But he kicked it up a notch. He used technology to speed up his extraction of the entire JSTOR database. He evaded network blocks in the process. When he finally could go no farther on Wifi he hooked his computer directly within the assumed-safe MIT subnet. In short, civil disobedience was taking too long for him and he decided to escalate.
So even if one agrees substantially with his desire for open access I hope it is understandable why people might disagree with his methods, and furthermore to understand why the legal system would disagree. We as a society have deliberately chosen to punish vigilantism because it breeds a world where justice applies only to those strong enough to enforce their worldview.
Although Aaron was not physically violent he certainly had a leg up on 99.9% of the rest of the U.S. population with regard to "cyberskills", does he not? If I stole a million cars and returned them without a scratch to their rightful owner in order to achieve some desirable positive goal I would still get in trouble, because I am not Caesar and therefore don't get to decide which laws do and do not apply to me (however virtuous I might be as a person).
We can debate about misdemeanor or felony, whether 3 months of prison or no jail time at all is appropriate but people seem to be shocked and amazed that the legal system would have taken an interest at all in this case, and I just don't understand why people think that.
My comment advocated neither. I merely pointed out that pubic prosecutions should only proceed if they are in the public interest. Hardly that radical.