Part of the answer here is to realize that the Catholic Church is not a monolithic entity in Northern Ireland. There was no single unified response to IRA activities.

On an official level, the Papacy distanced itself from the IRA and its violence. During Pope John Paul II's visit to the Republic, his homily at the Drogheda mass called for both sides "to turn away from the paths of violence and return to the ways of peace." Note here, this not an outright condemnation of the IRA itself, but of the violence they caused. The church also tried to end the Bobby Sands hunger strike and posed as a neutral arbiter between Sands and the Northern Irish prison system. Another factor complicating the Church's position within the Northern Irish state was that the latter's Catholic policy was religious-based; the Church had control over Catholic education and many social institutions within Catholic communities.

Local priests would occasionally denounce specific IRA actions from the pulpit when the IRA's violence would cross the line and negatively impact the Catholic community. One story from 1990 Derry exemplified how some of this opposition could occur. When an IRA member who was suspected of informing to the police, he disappeared. The IRA subsequently informed his wife that her husband would be fine so long as she does not go to her local priest, who they feared would denounce them. On the other hand, although it was uncommon, Catholic priests do appear within IRA brigade ranks.

But on the whole, the Northern Irish Catholic church was ambivalent towards the IRA. The existence of the IRA could be both a blessing and a curse. The IRA could protect Catholic communities from Protestant violence. The IRA also policed local Catholic neighborhoods against youth hooliganism or other crimes. However, policing by a paramilitary is a double-edged sword and their actions could step out of line. It's also worth mentioning that some IRA members saw Catholicism as less of a religious identity and more of an ethnic status. Some of the splinter factions of the IRA such INLA (Irish National Liberation Army which split with the official IRA during 1970s over the latter not being radical enough) had a quasi-Marxist political orientation that put it at odds with religious institutions.

Sources

Coogan, Tim Pat. The IRA: A History. Niwot, Colo: Roberts Rinehart Publishers, 1993.

Elliott, Marianne. The Catholics of Ulster: A History. New York: Basic Books, 2001.

English, Richard. Armed Struggle: The History of the IRA. Oxford: Oxford University Press, 2003.

Moloney, Ed. A Secret History of the IRA. New York: W.W. Norton, 2002.

Toolis, Kevin. Rebel Hearts: Journeys Within the IRA's Soul. New York: St. Martin's Press, 1996.

It's worth noting that the conflict in NI was largely a secular ethnic one, fought between the Irish and mainly the descendants of Scottish settlers (who settled privately and under the policy of the Crown in the beginning of the seventeenth century).