I'll paraphrase Churchill: I think that democracy is horrible, but it's simply the best means we have of protecting individual rights.
Furthermore, democracy doesn't mean "majoritarianism", it means "rule of people". Yet even a simple representative democracy is exceedingly difficult to implement (obvious example is how would one draw district boundaries to ensure fair representation of all groups -- Gerrymandering is a huge problem) as to adequately represent "the will of the people". So a lot of people are contending this specific point.
I think where I draw the line is in ends vs. means: I strongly care about protecting basic individual rights. Primitive ancestral tribalism means absolute collectivism and zero individual rights (the right to swing one's fist was not limited by where another's nose began), so we've continuously evolved better and better systems to do so including Anglo-American Common Law (which today still provides some of the strongest guarantees of liberty anywhere on Earth).
On the other hand, just looking at the judicial history, I see a lot of clever bending of the rules and hacks that got us there: using 14th amendment to apply first amendment to defend highly unpopular speech was both "anti-democratic" and contrary to the letter of the law (the first amendment clearly said "congress shall pass no law"). Likewise, Roe v. Wade was a great judicial hack (use of 9th and 14th amendment to defend another activity most everyone opposed) that significantly expanded women's reproductive freedom.
These kind of "hacks" even made the idea of law entertaining to me (when fresh out of undergrad, I was being prepared for deposition in some IP litigation I got dragged to as a result of an internship I had, the counsel seriously urged me to consider law school instead of MS in CSE). However, I knew that realistically my choices would be either near-starvation or big law (absolutely the wrong place for someone like me, who could never adhere to a strict schedule or a dress code).
However, I don't see that "order loving" and "order breaking" are mutually exclusive: a software engineer is free to work at a firm that requires everyone to be in the office at 9:30 (irrespective of how late they stay until) and many choose to do so (practically all engineer working for financial firms). I don't see an issue with companies choosing this culture, with some reasonable exceptions (e.g., I'm not a laissez-faire absolutist, so I would consider it grossly unjust to fire an engineer for coming at 9:45 because their daughter had a doctor's appointment that morning).
While I would abhor forced-collectivism as a political system, I've enjoyed working at smaller "collectivist" companies, i.e., where everyone is focused on the same goal (which benefits everyone) rather than on advancing themselves.
So where does aaron enter into this? I think to me the part I found morally repugnant that the law that was meant to defend JSTOR (who have dropped the charges and whose rights were not severely transgressed) was aimed disproportionally against Aaron. In other words the state was acting to some concrete end that went far beyond what was reasonable to protect individual rights.
If the state wanted Aaron to never do this again, clearly stating to Aaron that if this happens again he will go to jail (something that seemed to absolutely deter him) and get a felony on his record (something that, again, would clearly deter him -- in that it would make his goals of social activism much more difficult in terms of difficulty of finding employment, vote or run for office, etc...).
Everything else seems superflous, unneeded and disproportionate (if JSTOR pursued the case they would have had a right to some kind of settlement, but not, e.g., forcing Aaron to pay $2 bn or sending him to jail for a decade).
What I think energized me even more personally is that his situation is far from unique -- you were also one of the first to point to this out too. However, rather than forgetting about Aaron, the proper response is to further seize on the momentum: Aaron was certainly influential and this influence could be used to change the laws governing prosecutorial conduct. I think (but correct me if I am wrong), you would also agree with me here.
Where we disagree (as far as I understand your comments) is just because 51% of people find personal drug use repugnant (or believe cooky theories about it), than they have a free hand at imposing drug laws. My own take being that "unenumerated" individual liberties (liberty being defined negatively and circularly as something that doesn't infringe on the liberty of othes) should be restricted if and only if doing so is crucial to protecting the rights of others (e.g., to use an artificial example, if a pain killer happens to make 30% of its users instantly and extremely violent it can be restricted, as long as it is still available under supervised conditions to who can't for one reason or another use another pain killer). More fundamental liberties (those crucial to continuation of liberty itself -- free speech, protection against torture, protection against unreasonable search and seizure) should have an even stricter standard (something similar to the "clear and present danger" standard for free speech in the US today). I think it's also close to the fundamental framework most (but not all) HN-ers subscribe to (libertarians and liberals alike), but there is wide disagreement on specifics of how it applies in each individual case (it's clear that an outright ban on marijuana has a zero or negative effect as far protection of fundamental liberties of others goes, but it's a bit more difficult for other drugs). Some might also argue that there is an even more fundamental right to use an entheogen, etc...
The libertarian positions tend to be more categorical than the liberal ones (e.g., property is the more right, so taxation is always unjust, even if it's the only way to provide basic healthcare or legal protection for individuals).
I am hopefully not caricaturing you, but your argument seems to be that liberties and rights are crucial, but they are granted and limited based on "greater common good" analysis as opposed to more categorical statements. I think it's perfectly valid and (often) seems to lead to similar conclusions as the system I use, but the thought process is very different in that a deeper-level happiness of majority (which is usually greatly bolstered by liberty, but not always so), as opposed to liberty itself is your overriding concern ("if a small minority really wants to do X which poses no harm to the majority, but the majority is deeply upset that X is allowed, then it's fine to bring the legal system down full-force on the minority that chooses to do X").
In the end I think these two systems actually converge more often that not: drug war does not serve the common good, for example. Yet, it's the disagreements that can be particularly vehement (such as issue of laws that infringe on individual rights in one way or another, but yet have a clear societal benefit despite not immediately protecting individual rights -- e.g., seatbelt laws, laws regulating food portions, drugs beyond marijuana, certain police practices, etc...)
 Reasonable people can disagree whether academic publishers have a right to hold papers behind a paywall. I think that's debatable, with my own views being closer to Aaron's. Another example where this is simply hard and reasonable people coming from the same "first principles" can disagree.