See also Brian Tubbs' discussion at AC a little while back. And my follow up.
A few things I plan on looking into in the future: Hamilton tries to poison Seabury's well by associating his thoughts with Hobbes' and then cites a number of philosophers -- Grotius, Puffendorf, Locke, Montesquieu, and Burlemaqui -- who believed in "the law of nature" that supposedly contradicted the Farmer's position. Or at least, they contradict Hobbes' supposed atheistic absolutist notions. I haven't seen anything approaching a consensus among natural law philosophers showing they would have taken America's side against the British. I've looked into Aquinas' teachings on when laws and the authorities behind them may be resisted and I've found a very complicated, nuanced positions with lots of twists and turns. Anglicans like the Rev. Seabury accepted the authority of Richard Hooker (the Anglican heir to Aquinas); so it would be interesting to see if Hooker staked an explicit position on the matter.
In The Farmer Refuted, after trying to poison Seabury with Hobbes' well, Hamilton admits that the good Rev. was not, like Hobbes, an atheist. But that begs the question, was Hobbes really an atheist? I think it helps not to necessarily believe anything you've heard others claim about what a philosopher really thought (especially an enemy of the philosopher's teachings) but rather to read the philosopher himself. Hamilton apparently had a habit of wrongly accusing his political enemies of atheism as he did with Jefferson. Locke too was called an atheist. As far as I have seen, Hobbes, Locke, and Rousseau, all three self identified as Christians. All three likewise posited novel, controversial -- "modern" -- theories which might have lead traditional religious and political authorities to balk with, "atheist!", "deist!", or some other term of opprobrium.
I also wonder whether by attempting to poison the Farmer's well with Hobbesean atheism, Hamilton didn't grossly misrepresent what the Farmer wrote or meant by what he wrote. This is the passage with which Hamilton takes issue:
I wish you had explicitly declared to the public your ideas of the natural rights of mankind. Man in a state of nature may be considered as perfectly free from all restraints of law and government: And then the weak must submit to the strong. From such a state, I confess, I have a violent aversion. I think the form of government we lately enjoyed a much more eligible state to live in: And cannot help regretting our having lost it, by the equity, wisdom, and authority of the Congress, who have introduced in the room of it, confusion and violence; where all must submit to the power of a mob.
To which Hamilton replies:
The first thing that presents itself is a wish, that “I had, explicitly, declared to the public my ideas of the natural rights of mankind. Man, in a state of nature (you say), may be considered as perfectly free from all restraint of law and government; and then, the weak must submit to the strong.”
I shall, henceforth, begin to make some allowance for that enmity you have discovered to the natural rights of mankind. For, though ignorance of them, in this enlightened age, cannot be admitted as a sufficient excuse for you, yet it ought, in some measure, to extenuate your guilt. If you will follow my advice, there still may be hopes of your reformation. Apply yourself, without delay, to the study of the law of nature. I would recommend to your perusal, Grotius, Puffendorf, Locke, Montesquieu, and Burlemaqui. I might mention other excellent writers on this subject; but if you attend diligently to these, you will not require any others.
There is so strong a similitude between your political principles and those maintained by Mr. Hobbes, that, in judging from them, a person might very easily mistake you for a disciple of his. His opinion was exactly coincident with yours, relative to man in a state of nature. He held, as you do, that he was then perfectly free from all restraint of law and government. Moral obligation, according to him, is derived from the introduction of civil society; and there is no virtue but what is purely artificial, the mere contrivance of politicians for the maintenance of social intercourse. But the reason he ran into this absurd and impious doctrine was, that he disbelieved the existence of an intelligent, superintending principle, who is the governor, and will be the final judge, of the universe.
As you sometimes swear by Him that made you, I conclude your sentiments do not correspond with his in that which is the basis of the doctrine you both agree in; and this makes it impossible to imagine whence this congruity between you arises. To grant that there is a Supreme Intelligence who rules the world and has established laws to regulate the actions of His creatures, and still to assert that man, in a state of nature, may be considered as perfectly free from all restraints of law and government, appears, to a common understanding, altogether irreconcilable.
While it's true that the Farmer's view of the "state of nature" is closer to Hobbes', it in no way follows that this Hobbes like view of the state of nature is predicated on atheism (in which, again, Reverend Seabury did not believe). If anything, Hobbes' harsh view of the state of nature is closer to the traditional Christian doctrine of man's sinful nature. Indeed closer to Calvin's view of man as having a depraved nature. Locke's more cheery view of the state of nature was, if anything more modern and enlightened. And Hamilton recognizes this when he chastises the Farmer for not being up with "this enlightened age."