Apparently, the records of the local church in Brewster and the Unitarian Convention were incomplete on this point. This is to be expected since the mater did not proceed to a formal hearing. Part of the Horatio Alger formula is that the hero is falsely accused and loses his job because of manufactured evidence. The motivation for the false evidence is that someone wants the hero's job. The Horatio Alger hero leaves quietly without responding to the charges.
Later events exonerate the hero.
This element of the formula dates from the time of the Brewster episode. The friar achieves some sort of peace, realizing the world will be a better place if he continues to live and continues his ministry. For Alger, writing for boys was his ministry. Thus Horatio Alger seems to have made a veiled but vigorous denial of the charges against him and at the same time admitted a significant moral lapse. Raymond Feist, the science fiction writer, has used some Horatio Alger themes in the Serpent War Saga.