RKBA is based on the idea that an armed society is a free society and capable of controlling the government.
Individual self defense is secondary and incidental to that from what I've read in the Federalist and Anti-Federalist papers.
I think you have the order reversed. In principle, we have the absolute right to self-defense regardless of what may be written on a piece of paper. In other words, the 2nd merely codifies an existing right. Since the 2nd helps ensure that individuals are supreme, all other organizations (such as government), are subsidiary to this order.
In order for individuals to associate freely in an open society, we have a wide range of laws in which to regulate behaviour. This includes the principles of private property and threats to bodily harm. Absent any violation of these two elements, our poster is actually running the risk of being arrested himself; a veiled threat is still a threat.
Neither the Federalist nor the Anti-Federalist papers address the Bill of Rights--they only address the text of the un-amended Constitution. If you want to understand the Federal Constitution's Bill of Rights, the place to look is at the pre-Constitution Bills of Rights of the various states. The best statement is from the Connecticut state constitution (paraphrasing, as I don't have the exact quote handy) "that the people have the right to keep and bear arms for defense of themselves and their own state, and the taking of game". Self defense, militia duty, and hunting were ALL reasons for codifying the RKBA.