Small differences between religious confessions always sufficed for violent conflicts. (Between protestants and catholics the base of differences worked very often as explanation for wars.) You can't make this clear cut between religion und politics.
Northern Ireland is a modern society, therefore the religious differences are not the key reasons, but the religion has a big influence as dividing factor, which enhances the gap between the two groups and exacerbates a rapprochement.
The conflict in its core is not really a confession war, but it follows a ideological logic, which seems kind of religious.

The attitude of the IRA is affected by the religious feeling of beeing justified for violence. This holy war of the IRA for a united Ireland shares some motives of the crusades, who also chased the "infidel oppressor".
In Cal this attitude is shown in the lesson by the priest, when he say: "There is such a thing as righteous anger", while the punishment of the "sinner".

Cal is not religious in the core meaning, but he internalized the Christian believing of moral supremacy. This helps Cal/ IRA to legitimize his deeds as unavoidably.