Sometime between August 1843 and April 1844 Fr William John Burke converted from a Catholic to the Protestant faith. It was not uncommon at the time. There were quite a few church missions across the country such as those set up by Alexander Dallas and Edward Nagle.
Many organisations were established in the early nineteenth century to convert Irish Catholics to Scriptural Protestantism. some, such as the Irish Society (1818) and the Achill Mission (1834) were run by members of the Church of Ireland while others were undertaken by Protestant mission of other denominations… The Irish Society was also active in north Mayo…
The Mission spread to some areas in Co. Galway and this is possibly where William John Burke converted. Whether he sought them out or it was the other way round in April 1844 he was back in his home parish of Kinvara renouncing Catholicism from the altar.
…On 22 April 1844 he renounced the Catholic Church and became a minister of the Church of Ireland. The scene of this extraordinary occurrence was the little Protestant Church that once stood across the street from the present Community Centre…
The paper carried the following report of the incidence.
We learn that the Rev. William John Burke, who for the last thirteen years has been a Romish priest, publicly red his recantation, and conformed to the united Church of England and Ireland, in St. John’s Church, Kinvarra, in the county Clare, on Sunday last. During the return of the Rev. Mr Burke, from Church, in the carriage with the two clergymen, the Rev. Mr. Moran and the Rev. Mr. Nason, who had been present at the ceremony, a mob of nearly two thousand persons, we are informed, assembled with shouting as the party passed, and threw several stones at the carriage. One of them struck the carriage, but the party being well armed, and defended by a body of police, escaped serious consequences. Such is the genius of Popery. – Dublin Statesman
This incident alone was enough to discredit the William John Burke in the eyes of his enemies but, another event was about to unfold. Although he did his best to keep it quiet his secret got out and his enemies found out. It did not take long for William John Burke to be arrested and tried at the Galway Assizes accused of a felony, which carried the sentence of transportation to Australia.