Few things:

1) To be honest I'm not the biggest fan of arguing about overthrowing US government, as:

a) Very few people (certainly not me) are willing to risk their lives for abstract ideas. In other words, this would have to be a fairly significant encroachment, e.g., suspension of all civil rights or a military junta coming into power (arguably, this almost happened in the 1930s: http://en.wikipedia.org/wiki/Business_Plot): the point is to use first amendment etc... first to prevent it from getting that point.

Yet, a lot of people don't even bother to research the issue, or vote (even for a protest candidate). Vast majority of people don't know what "14th amendment incorporation" is, or that Iraq did not actually have WMDs. So overriding political apathy is and defending encroachments of any civil rights is more important to me: instead of panic buying firearms, people's money is better spent donating to ACLU, EFF, and SAF.

b) The preamble does not mean that being part of a militia capable of challenging the federal government is the only legitimate reason for firearm ownership. In essence it's as if first amendment was prefixed with "Excellent newspapers being necessary for..." -- I don't think an intellectually honest person would use this to argue that it should exclude any other medium of expression, any more that constitution explicitly authorizing an army and a navy doesn't mean it's unconstitutional to create an air force.

However, given that individuals serving in state militias (which, again, were not intended strictly to take on the federal government) required individuals to bring their own firearms -- it does suggest that firearms in common civilian usage should not be restricted in a way that prohibits common legitimate civilian firearm use. Note that this is still leaves a lot of place for gun control, regulation, and further rulings.

2) You're making the assumption that if such a scenario does happen (again, something I don't think about much myself), the citizens will be fighting the full force of US government all by themselves without any popular support.

Well, first if that is they case, they're probably an extremist group that deserves to lose. If they have wide popular support and the backing of another power (as was case during Mexican revolution), the civilian firearms would only serve as a means to gain access to a fuller range of options and/or to "join forces" with significant factions of US armed forces that would defect. I'm pretty certain that if given orders to suspend the entire Bill of Rights nationally, most of US military and police would refuse to follow them: irregular civilian groups trapped in pockets that do "follow orders" would be able to use common firearms (these could even be bolt action rifles) to break to rebel controlled territory.

Again, though, I'm not too comfortable arguing this: it's probably more likely that deprived of education, apathetic about politics, yet given sufficient electronic toys, "bread and circuses", and yes -- firearms to fulfill their commando fantasies -- the populace would simply vote to repeal The Bill of Rights. This is something I'm far more afraid of.

I don't want to fight this on HN, but here's why I hold the views that I hold:

I remember a time in high school AP US History class: it was a mock "re-trial" of a famous free speech case and I was chosen to "play" the role of Clarence Darrow. I argued that first amendment protects a near absolute right to free speech ("clear and present" danger being the limit).

Somebody in the audience, however, said that "If you use this argument with the first amendment, what does this mean for the second amendment and guns?". This was shortly after Columbine and long before Heller, so I gave the standard "second amendment is a collective right" response.

However, deep down I felt it was a bullshit response. It got me an A, but I later learned that this probably not what Clarence Darrow would argue: http://law2.umkc.edu/faculty/projects/ftrials/trialheroes/Da...). First ten amendments are not arbitrary, they represent the analogue of the English Bill of Rights that constitution itself did not include.

That has a few implications. First, we can't simply equivocate it away by reading the constitution to read what we want to read it. Now if you do indeed feel that the second amendments prohibits what would otherwise be good public policy, then argue for its repeal. However, I'm very uncomfortable with this idea for a simple reason: every single fundamental right in the bill of rights can be exercised in a dangerous manner (especially the first) or comes into conflict with security (government's legitimate role in reduction of violence).

Were the founders right to include the second amendment? I don't know, but I am not comfortable with -- for the first time in US history -- repealing a fundamental liberty. You can try equating it with slavery, but you know that's b.s. -- slavery involves coercing another human being, the lone act of possessing a firearm does not.

There are certainly limits on the second amendment (much like there are limits on the first amendment): no one disagrees that certain people should not be allowed to own firearms or that especially dangerous and unusual firearms can be banned.

See another comment I made on this matter on how this thinking fits into more concrete policy ideas: http://news.ycombinator.com/item?id=5070170 (tl;dr background checks on 100% of purchases -- good, more authority to stop and investigate straw purchases and weapon trafficking -- great, assault weapon bans -- pointless and dangerous)