Stand against persecution (1657–73)
In September 1657, the Commissioners issued a letter, to the authorities of Rhode Island, demanding the suppression of the Quakers; of all the Commissioners, Cudworth alone refused to sign. In December (tenth month, Old Style) 1658, he wrote a long letter (to a person in England), in which he provided details of the brutally harsh and (as he considered) illegal laws and punishments meted out to the Quakers (and others) who the Puritan monopoly in the colonial legislature wished to purge. He reported that this "Antichristian Persecuting Spirit" had been at work during the previous two years (during his magistracy), and that he had often had to object to such proceedings (though in a respectful manner). His objections had given rise to a petition against him (signed by 19 people, who complained that he had entertained Quakers at his house). This, he admitted, he had done to acquaint himself with Quaker principles (rather than to condemn them out of prejudice); and he found that he disagreed with the Quakers on various matters, and told the court, which heard the petition (presided over by Thomas Prence), that he was no Quaker: but that, just "as I was no Quaker, so I will be no Persecutor".
When the Act of Court was read before the people at Scituate (and before the Scituate Military Company (of which he was head)), there was a great disturbance against him, which he brought under control by making a speech. Consequently, a fresh petition was brought (signed by 54 hands), to which the court answered respectfully that Cudworth was a very useful and accomplished person, and that the only point against him was his association with Quakers (One or other of these petitions from "sundry persons from the towne of Scituate" was noted in the General Court (March 2, 1657/58)). In consequence of this, he and his friend Hatherly had been removed from the Bench at the previous election, and Cudworth himself was relieved of his military command (with Lt James Torrey and Ensign John Williams subsequently ordered to assume command of the company).
The persecutions to which Cudworth referred were (he stated) fuelled by the actions of the Boston legislature (then led by John Endecott). Cudworth's uncle, Israel Stoughton (d.1644), had worked with Endecott during the period of the Antinomian Controversy surrounding Anne Hutchinson, but had returned to England. Israel's son, William Stoughton (later involved in the Salem witch trials) was, during the 1650s, also resident in England. It was the voyage from England of the Speedwell in 1656 (which brought eight Quakers who were immediately imprisoned and expelled), and of the Woodhouse in 1657, and the subsequent renewal of their attempts to enter the Massachusetts Bay Colony from Rhode Island or Barbados, which now aroused the Puritan hostility. The treatment of Quakers (such as Christopher Holder, who was flogged, imprisoned, and had an ear cut-off) under Boston laws (and their law of banishment on pain of death), whipped up similar fervor elsewhere in the United Colonies in imitation: laws were emended retrospectively so that even minor actions of dissent and, of course, the Quaker refusal to take oaths were punishable by cumulative fines and imprisonments resulting in the eprivation of livelihood. Cudworth noted the strong influence of Quakerism upon the people of Sandwich, in Barnstable County.
At the time of the petitions against Cudworth (March 1657/58), the Rhode Island Assembly (upholding their principle of freedom of consciences) rebuked the United Colonies Commissioners for their demand concerning preventing the admission of Quakers, and warned that any subsequent civil troubles should be referred to "The Supream Authority of England". Cudworth's letter, written weeks after the death of Oliver Cromwell (September 3, 1658), naming the relevant members of the legislature and accusing them of arbitrary legislation outside the principles of English law, may reflect this intention. For disobedience to their laws, the Boston authorities executed: William Robinson and Marmaduke Stephenson (October 1659), Mary Dyer (1 June 1660), and William Leddra (March 1661).
In 1659, James Cudworth was sent, by Scituate, as a Deputy to the Plymouth General Court, but was not approved by the Court. Charged with disaffection to authority (on the evidence of a copy of his letter), he was ordered to appear before the Court (March 1660) on a bond of £500, and was sentenced (6 June 1660) to be disfranchised of his freedom of Plymouth Colony, having been found a "manifest opposer of the laws of government". In October 1660, he was questioned concerning a letter of reply received from John Browne of Frampton. In the light of the information which reached England, a lengthy indictment of the persecutions against Quakers in New England was published in London by George Bishop, entitled New-England Judged (1661), with a supplement describing the sufferings of the martyrs, and a full second part was published in 1667. The first volume (1661) of Bishop's work included the first publication of Cudworth's letter: it was this, therefore, which may have been influential in causing Charles II (following the Restoration of the English Monarchy (1660)), to issue "The King's Missive" (9 September 1661), which required that any Quakers held by them under sentence of death or other corporeal punishment should forthwith not be proceeded against, but should be returned (at once) to England where the charges against them might be considered according to English law.
Before this, in March 1660/61, Cudworth's elder daughter, Mary, had married the Quaker, Robert Whitcomb, and had been fined for disorderly marriage and for choosing each other without parental consent. They were, however, permitted to marry in orderly fashion (the principal objection being to Mr Henry Hobson, who had derided their authority by the counterfeit solemnization). In 1665, Cudworth's eldest son, James, also married a Quaker, Mary Howland, and they were fined for fornication (Cudworth's consent or otherwise is not noted).