For a number of years, Thayer was involved in a dispute with James G. Carter, then-Deacon of Thayer's congregation and later a member of the Massachusetts House of Representatives, over the latter's refusal to return funds donated toward the establishment of an instructional academy that failed to materialise. Thayer publicly denounced Carter's actions and called on him to reimburse donors of the failed project. Carter, however, refused and was eventually removed from his position as the church's Deacon. Messerli (1965) argues that Carter's alienation of Thayer (and, by extension, most of the state's clergy) significantly contributed to his loss to Horace Mann in the 1837 election for the position of Secretary of the just-established Massachusetts Board of Education, the first state board of education in the United States.