I don't think Barton ever called Tom Paine a Christian, just the opposite.
Paine later published his Age of Reason, which infuriated many of the Founding Fathers. John Adams wrote, The Christian religion is, above all the religions that ever prevailed or existed in ancient or modern times, the religion of wisdom, virtue, equity and humanity, let the Blackguard Paine say what he will. Samuel Adams wrote Paine a stiff rebuke, telling him, [W]hen I heard you had turned your mind to a defence of infidelity, I felt myself much astonished and more grieved that you had attempted a measure so injurious to the feelings and so repugnant to the true interest of so great a part of the citizens of the United States.
Benjamin Rush, signer of the Declaration, wrote to his friend and signer of the Constitution John Dickinson that Paine's Age of Reason was absurd and impious; Charles Carroll, a signer of the Declaration, described Paine's work as blasphemous writings against the Christian religion; John Witherspoon said that Paine was ignorant of human nature as well as an enemy to the Christian faith; John Quincy Adams declared that Mr. Paine has departed altogether from the principles of the Revolution"; and Elias Boudinot, President of Congress, even published the Age of Revelationa full-length rebuttal to Paine's work. Patrick Henry, too, wrote a refutation of Paine's work which he described as the puny efforts of Paine.
When William Paterson, signer of the Constitution and a Justice on the U. S. Supreme Court, learned that some Americans seemed to agree with Paine's work, he thundered, Infatuated Americans, why renounce your country, your religion, and your God? Zephaniah Swift, author of America's first law book, noted, He has the impudence and effrontery to address to the citizens of the United States of America a paltry performance which is intended to shake their faith in the religion of their fathers. John Jay, an author of the Federalist Papers and the original Chief-Justice of the U. S. Supreme Court, was comforted by the fact that Christianity would prevail despite Paine's attack,I have long been of the opinion that the evidence of the truth of Christianity requires only to be carefully examined to produce conviction in candid minds. In fact, Paine's views caused such vehement public opposition that he spent his last years in New York as an outcast in social ostracism and was buried in a farm field because no American cemetery would accept his remains.