Hmmm, I am reading it slightly differently than both you and the article as I reflect upon the points made in the article.
I think "well regulated" means directly controlled by the federal government, and "militia" means the military that the federal government controls. By "necessary for a free state" I take it to mean that in order to secure national security, we need to give the federal government to power to have such a militia.
I take the inherent danger of having a regular military controlled the federal government to go without saying.
In modern vernacular I would say the amendment would read:
"Since the feds need to have a regular military under their command in order to keep our country secure, it would be insane to leave everybody vulnerable to the abuse of that controlled military by infringing on their God given right to keep and bear their own arms"
“I think “well regulated” means directly controlled by the federal government”
The word ‘regulated’ when written didn’t have that meaning of ‘controlled’. It meant more of ‘functional’ or ‘capable’, just like the word ‘militia’ didn’t mean a formal army but meant the body of men useful for defense, but not necessarily a formal army of any sort.
So, your conclusion that we have arms to defend against the federal government is true but that is only one part of the 2nd. The first part is that We the People are the primary force for national defense, to be called upon by governors and the President alike, to be trained and equipped if necessary, but, as you concluded, to also be part of a force that could resist an out of control federal army.
The 2nd has that dual purpose as I read it and read the words of the founders that wrote it.