He studied for three years in the Theological Department of Yale College, and was licensed to preach in 1844.
MacWhorter received deacon's orders in the Protestant Episcopal Church, May 31, 1863, at the hands of Bishop Potter of New York.
He published a volume entitled Yahveh Christ, or the Memonal Name, besides several magazine articles on metaphysical and theological subjects.
In 1847, MacWhorter was embroiled in a noted scandal of the day, the subject of Catharine Beecher's book Truth Stranger than Fiction (1850).
MacWhorter had become friends with a fellow lodger at New Haven's Tontine Hotel, the older, unmarried author Delia Bacon, who would later be notable for her speculative writing about the Shakespeare authorship question.