Joseph Story did NOT consider the militia to be the only way to arm the people, but instead an outgrowth from the right of citizens to keep and bear arms. Here is the full paragraph:
1890. The importance of this article will scarcely be doubted by any persons, who have duly reflected upon the subject. The militia is the natural defence of a free country against sudden foreign invasions, domestic insurrections, and domestic usurpations of power by rulers. It is against sound policy for a free people to keep up large military establishments and standing armies in time of peace, both from the enormous expenses, with which they are attended, and the facile means, which they afford to ambitious and unprincipled rulers, to subvert the government, or trample upon the rights of the people. The right of the citizens to keep and bear arms has justly been considered, as the palladium of the liberties of a republic; since it offers a strong moral check against the usurpation and arbitrary power of rulers; and will generally, even if these are successful in the first instance, enable the people to resist and triumph over them. And yet, though this truth would seem so clear, and the importance of a well regulated militia would seem so undeniable, it cannot be disguised, that among the American people there is a growing indifference to any system of militia discipline, and a strong disposition, from a sense of its burthens, to be rid of all regulations. How it is practicable to keep the people duly armed without some organization, it is difficult to see. There is certainly no small danger, that indifference may lead to disgust, and disgust to contempt; and thus gradually undermine all the protection intended by this clause of our national bill of rights.
http://press-pubs.uchicago.edu/founders/documents/amendIIs10.html
Anyone who can argue that "citizens" in this paragraph actually means "militia" is not interested in facts that conflict with his beliefs. Story is stating that without the individual right, the militia can't exist. In other words, "Militia" is a subset of "citizens", not the other way around. The "duly armed" clause ties to his worry about whether or not the militia itself would be of much use without good regulations, and has no bearing at all on the individual citizen's right to keep and bear arms. Without the militia, the individual right still exists.
As for your reference in another post to Blackstone not equating "having arms" to an individual right, here is a copy from Blackstone's "Commentaries on the Laws of England", book 1, chapter 1:
The fifth and last auxiliary right of the subject, that I shall at present mention, is that of having arms for their defense, suitable to their condition and degree, and such as are allowed by law. Which is also declared by the same statute I W. & M. st.2. c. 2. and is indeed a public allowance, under due restrictions, of the natural right of resistance and self-preservation, when the sanctions of society and laws are found insufficient to restrain the violence of oppression.
In these several articles consist the rights, or, as they are frequently termed, the liberties of Englishmen: liberties more generally talked of, than thoroughly understood; and yet highly necessary to be perfectly known and considered by every man of rank or property, lest his ignorance of the points whereon it is founded should hurry him into faction and licentiousness on the one hand, or a pusillanimous indifference and criminal submission on the other. And we have seen that these rights consist, primarily, in the free enjoyment of personal security, of personal liberty, and of private property. so long as these remain inviolate, the subject is perfectly free; for every species of compulsive tyranny and oppression must act in opposition to one or other of these rights, having no other object upon which it can possibly be employed. To preserve these from violation, it is necessary that the constitution of parliaments be supported in its full vigor; and limits certainly known, be set to the royal prerogative. And, lastly, to vindicate these rights, when actually violated or attacked, the subjects of England are entitled, in the first place, to the regular administration and free course of justice in the courts and law; next to the right of petitioning the king and parliament for redress of grievances; and lastly to the right of having and using arms for self-preservation and defense. And all these rights and liberties it is our birthright to enjoy entire; unless where the laws of our country have laid them under necessary restraints. Restraints in themselves so gentle and moderate, as will appear upon farther inquiry, that no man of sense or probity would wish to see them slackened. For all of us have it in our choice to do everything that a good man would desire to do; and are restrained from nothing, but what would be pernicious either to ourselves or our fellow citizens. So that this review of our situation may fully justify the observation of a learned French author, who indeed generally both thought and wrote in the spirit of genuine freedom;48 and who has not scrupled to profess, even in the very bosom of his native country, that the English is the only nation in the world, where political or civil liberty is direct end of its constitution. Recommending therefore to the student in our laws a farther and more accurate search into this extensive and important title, I shall close my remarks upon it with the expiring
wish of the famous father Paul to his country, “ESTO PERPETUA!” [“ENDURE FOREVER!”]
http://lonang.com/library/reference/blackstone-commentaries-law-england/bla-101/
Since you depended upon others for the part about Blackstone and having arms, it wouldn't be fair to call you on it. However, in the future you might want to research your POV before posting to ensure that it will stand up to scrutiny.
I'm still recovering from surgery, so I'll leave it for now. Back to my generic Vicodin... 
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