A great deal has been said about the Founders and their disdain for standing armies. A standing army was obviously provided for in the Constitution. It was left to the individual States to organize and officer their own Militias. As you have highlighted there was popular resistance to federal arming/disarming of the Militias. After the NG was formed subsequent legislation provided that enrollment in each State's NG was also simultaneous enrollment in the NG of the United States.
During the 19th century the several States grew closer due to advances in travel and communications. As economic cooperation began to demonstrate, specialization made sense and certain sacrifices would improve the overall condition of the general welfare of the People. This was true of military/Militia as well.
During the early 20th century, due to the numerous wars and the increasing acceptance of US involvement in foreign affairs, the People accepted the idea of a large standing federal force. These evolutions from State Militias to a standing federal army demonstrate an acceptance by the American People of this country's world involvement and their trust of the federal government.
Whatever the structure of the main federal force, its composition, membership and officers are drawn from the civilian People of the several States. It can't be argued that such a force intrinsically benefits by restricting arms from non-members.
The 2A is part of the BoR. The BoR exists to protect individual rights from government abuse. This is evident by the nature of the other articles protecting such personal rights as free speech and privacy. Whatever other consequences devolve from the 2A, it acts as a protection for personal rights. It may have helped secure the ability of the People to participate in a militia. It may have enabled hunters to hunt. The essential nature of a right is as an attribute of a person. The nature of people doesn't change due to the evolution of their government. It is stated in the Declaration that "--That whenever any Form of Government becomes destructive of these ends, it is the Right of the People to alter or to abolish it". The evolution and continued development of our government is a basic strength. Providing for government to adapt to and better serve the People is a strength. The People will always have an individual RKBA.
Most basically the People have a right to life and have a right to protect themselves.
Have a great day. 
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