Henry VIII introduced Protestantism and firmly established British rule. He reorganized the way property was distributed doing away with the customs of Brehon Law and common ownership of property. Irish chiefs were to surrender the tribal lands in exchange for the regranting of those lands to them personally. Thus for example, "the chief of the Ulster O'Neills, Con, submitted on this basis in December 1541, taking the title of Earl of Tyrone ahd having his eldest son recognized as his successor" rather than his other son or his nephews who had legitimate claims under Gaelic law (82). Protestantism initially did not have a strong foundation as there were few towns and no strong middle class, which traditionally formed the basis of that congregation. In 1592 Queen Elizabeth I established Trinity College as part of an attempt to "counteract the growing tendency for young Irishmen to journey to universities in Catholic Europe where they could learn seditious ways" (85).
At one point Catholicism and the cause of a 'free Ireland' were synonymous and so the English government sought to suppress this by means of excluding Catholics from serving in government and banning Catholic priests from Ireland (100-101). By the 1690s Irish parliament was completely Protestant. In 1695 the Irish government began enactng the Penal Laws against Roman Catholics in Ireland. These laws were completed by 1727 and lasted about 100 years (114-115).
"By the end of the seventeenth century, Ireland had effectively been conquered. Almost every generation during the previous two hundred years had experienced military, economic and political attacks" (115). At this time and through the 18th century, the native Irish were treated little better than slaves. Reform through the efforts of Wolfe Tone enacted the Catholic Relief Act of 1793 which gave propertied Catholics the "right to vote and enter the professions, though not to stand in elections" (134).
In the 1800s the drive for Irish nationalism (e.g., Irish Republican Brotherhood) somehow pushed the church to identify more and more with the British government (171). "The Church became increasingly hostile to any movement that threatened the political or social status quo. Not until 1886 did the Church formally endorse home rule for Ireland, and even then only as 'representing the legitimate aspirations of the Irish people.' To the Church, legitimacy meant remaining within the framework of British law and practice. It rapidly distance itself from rebellious nationalism after [Daniel] O'Connell's early successes, condemning the Fenians, the 1916 Rising and, in 1920, the IRA. In return for Catholic Bishops' influence on behalf of constitutionalism in Ireland, successive British governments acknowledged the special position of the Church: a position so strong that in 1885 the Church secured the Irish Party's acceptance of a major voice for the clergy in the selection of parliamentary candidates" (172).
If as these excerpts suggest that the church was involving itself in politics, then the religious aspect of the church seems to be tainted. The church is giving unto Rome its due, yet neglecting the due owed to God. No wonder there is ambivalence in Stephen.
Ranelagh, John. Ireland An Illustrated History. New York: Oxford, 1981.