I know things were/are a lot more complicated than just "Protestant = Unionist, "Catholic = Nationalist", but the religious difference certainly did not aid matters.
The fact that most Irishmen were loyal to the Catholic Church, at a time when the Pope called on Catholics to revolt against Elizabeth I (in his bull
Regnans in Excelsis) made the religious difference highly problematic. It made the Irish pawns in the English/Spanish struggle and ultimately convinced Elizabeth and her successors that the way to pacify Ireland was to flood it with English/Scottish settlers.
I think the best way to make Ireland loyal to the Crown is to have Protestantism make inroads by this time. As noted above, an earlier translation of the Bible into Irish might have helped. If Edward VI had outlived his sister Mary, leading to a seamless religious transition to Elizabeth, that may have helped as well; in OTL, the re-established Church of England under Elizabeth had a serious shortage of trained clergymen in its early years. If we have Edward live to 1558 or sometime later, the C of E can have a more established clergy by the time Elizabeth takes over and may be able to launch more effective missionary efforts in Ireland.