Even if the term DOES mean “under control of the government”, it still works our way.
A valid interpretation of the 2ndA amounts to “even though we grudgingly acknowledge a standing army is necessary, the people STILL have an inalienable right to own military weapons”. The Founding Fathers disliked the idea of a standing army, but realized one was necessary (armed populace is great in theory, but not reliable come organized international warfare). In granting the government the power to raise and maintain a standing army, they clarified that doing so in no way justified disarming the populace.
The awkward wording makes more sense this way, and still comes to the same conclusion.
Here's a link:http://www.largo.org/literary.html
I would disagree that the construction of the sentence is awkward at all, especially for our Founders, many of whom were trained in the classics. The militia phrase is a common construct in Latin and is known as an absolute clause.
The relationship between the militia clause and the rest of the sentence is intended to be unstated and such that the dependent clause does not change the meaning or intention of the independent clause.