All the rights that you lose when Congress has the power to "discipline" you outside of the judicial system.
But that section (Article 1, Section 8) differentiates between "the militia" and the part of the militia "employed in the service of the United States":
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,
Apparently, whatever "the militia" refers to, it's still "the militia" even when it's not in active service.
That article also gives "disciplining the militia" and "governing the militia on active service" (paraphrased) as separate powers of Congress. Presumably, these mean two different things.
When it comes to the Second Amemdment, you argued that "the militia" equalled "the people". Now, when it comes to Section 1, you're arguing that "the militia" only includes people "when they are acting as the militia"; which is it? Which do you think the Constitution means when it says "militia"?