Our system says we have to abide by SCOTUS decisions, but that doesn't mean they have decided correctly. Either in a general moral sense, or in the stricter sense of correctly interpreting law.
If that were true, we'd have to live with Plessy v. Ferguson, or consider Citizens United a masterpiece of jurisprudence. Stare decisis applies, but the Court does reverse itself, or we'd be stuck with Plessy and never have had Brown vs. Board.
So, though I've had these arguments with many folk many times, what Justice Scalia or others on SCOTUS believe do not negate that the Constitution discusses the very Militia the 2nd amendment references. Thus, there is an easy way to understand what is being referred to; it's mentioned elsewhere in the document.
This is one of those specifically enumerated powers conservatives/originalists love to talk about; this is something the Constitution directly and specifically says government must do.
Article I Section 8 clause 15:
To provide for organizing, arming, and disciplining, the Militia, and for governing such Part of them as may be employed in the Service of the United States, reserving to the States respectively, the Appointment of the Officers, and the Authority of training the Militia according to the discipline prescribed by Congress;
Also see: Militia Act of 1792:
http://www.constitution.org/mil/mil_act_1792.htm
Like I've said 8000 times, and will repeat, though the militia was called up from the people, not all people were considered eligible, and were not part of it until the executive authority did so, and that militia was supposed to be disciplined, one source of discipline being regulation of the firearms they had access to.
Also, BTW, despite what some mouth-foamers claim, one of the key functions of the militia was to PUT DOWN insurrections AGAINST the government. NOT OVERTHROW IT.