Did the Native Americans have a right to bear arms? Do you really think the average American citizen today is better armed than the American military. How did the Iraqi Army do against them? It seems to me you must be engaged in some sort of internal rationalizations. Seems to me that the only real impediment to a coup by the military is the absence of the wish for it.
Perhaps you don't like the fact that the motive you state for why we have the second amendment has been rendered ridiculous, both in reality and in the minds of the people.
It strikes me that we have had a compromise of opinions on the 2nd for many many years now. You can't own machine guns and in California we are limited to 10 shot clips. So it would seem that the fear of the individual madman killing multiple scores of people, hiding behind his right to bear arms, is already beginning to be restricted. How do you think a lead lined gun that fires a single plutonium bb would go over legally? Not too well, I would suspect.
The rationalization you use for the reduction in rights is to save the ~5k of non-gang, non-crime, non-suicide deaths per year which may or may not have occurred anyway without a gun. Furthermore, the rationalization you use is a reduction in homicides, which hasn't been supported by Australia or other countries, nor have violent crimes committed through other means.
So that's your rationalization, eliminate rights for a few thousand deaths which will likely occur anyway. You could require ignition interlock on every single vehicle to probably nearly 100% eliminate DWI related accidents and fatalities and save more lives. How about that?
What about banning smoking. There's millions of lung cancer and other smoking related deaths eliminated. What about Bloomberg's Big Gulp ban, or shit, just ban sugar and require a minimum of 1hr of exercise a day, subject to jail time. You'll prevent millions upon millions of diabetes or obesity related fatalities.
Just how far would you be willing to go?
And on the topic of defense against governments (including our own), the size of the US military is pretty small compared to the size of the armed US population. 100mm people fighting against the government, not concentrated in one space, would be very difficult to battle, even with modern weapons. Especially considering various laws. It wouldn't be nearly as clean as the Civil War since the differences are ideological, not really geological.
The notion may be somewhat far fetched, but the idea that we would go quietly as herded sheep would be gone.