Actually, it was during the War of 1812 that the militias were found inferior to a federal army. When the war was over, the militias essentially went away as a separate fighting force.
Yes, the citizen was to be armed -- at least, those who fit the definition (males between a certain age). They were to be armed, they had a right to be armed, because they may be needed to secure a free state. It was that right that was protected from infringement by the federal government.
Yes, that right is protected. Those rights still stand under the Constitution. According to the Constitution, it's vital for the citizens to be able rise and defend themselves, outside of the Army, if necessary. And unless citizens can keep their own arms, there's no way that can happen.