Throughout his life, Morse was much occupied with religious controversy, and in upholding the faith of the New England church against the assaults of Unitarianism. Ultimately his persevering opposition to liberal views of religion brought on him a persecution that affected deeply his naturally delicate health. He was very active in 1804 in the movement that resulted in enlarging the Massachusetts general assembly of Congregational ministers, and in 1805 unsuccessfully opposed, as a member of the board of overseers, the election of Henry Ware to the Hollis Chair of Divinity at Harvard.