Do you remember something called the "Revolutionary War"? It was an event in history that happened when the people who wrote the 2nd amendment fought the British government for control of the country.
It does though. Things were quite different when the constitution was written. The federal government was never supposed to wield absolute power over the states. "...consent of the governed..." etc. It's pretty clear that they believed that a populace should be able to abolish their own government - they did so themselves.