It was the traditional Andalusian peasantry/tenant farmers, many of which worked on land the the Church had enjoyed a monopoly on since the reconquest, who were most violent toward the Church. These were not "communist agents" but just the angry "common people" taking arms against the aristocratic Church.
The actualy military civil war was indeed between a "right" comprised of landowners, aristocrats, and the Church versus the southern peasantry, the proletariat, and various leftist groups, the latter of which wound up in civil war once the Soviets got involved.
That being said, more people were killed by the White Terror of Franco than by the Red Terror in Andalucia. He even had the Luftwaffe firebomb the devout Catholics of the Basque Country because they wanted to preserve their traditional cultural/political autonomy.
It should be no surprise that so many Spaniards became anti-religious after the Franco years, and his glorification of an idealized/rural past did not jibe well with a 20th century urban society. All the Catholics who whine about how the left has "destroyed" the clerical authoritarian regime fail to acknowledge that it is the Spanish people themselves who have rejected the RCC, largely due to its perceived irrelevance, as well as its support for the Franco regime.
I'm not one to defend Franco completely, but he was certainly the "lesser evil" of the two.
All the Catholics who whine about how the left has "destroyed" the clerical authoritarian regime fail to acknowledge that it is the Spanish people themselves who have rejected the RCC, largely due to its perceived irrelevance, as well as its support for the Franco regime.
It's a lot more complicated than that. There's also the cultural war from the 1960s onwards that manifested itself much more virulently after Franco died. Despite all that, you still get millions of people in Spain who stood with the Church at recent pro-life rallies.
As a conservative, you shouldn't be defending these leftists, because they're only setting up something worse- the reconquest of Spain by the Muslims.
Hitler was the one who had the Luftwaffe bomb Guernica, and in fact this was one of the things that led Franco to remain neutral in WWII; he was not even informed of the bombing until it had occurred, and would never have approved it. Franco was a Spanish nationalist, and did not appreciate having someone come in and destroy his country and his people.
The peasants were not the ones who, as you put it, “took arms against an aristocratic Church.” Any reaction to the Church depended largely on the extent of Communist labor activities among the workers of a particular area, and the worst by far were the Communist-influenced workers of Barcelona. And what they attacked first, in the usual program of “miserification,” were Church schools, religious orders that ran charitable activities, and individual priests and layleaders, particularly those involved in social and charitable works. This was all motivated by the Communists, who had been active in Spain for decades before the war and in fact who attained dominance only through electoral manipulations and the failure of the Church to offer any political support to the opponents of Communism.
The Church was just fine under Franco and had about the same level of anti-Catholicism (mostly anti-clericalism) as any majority Catholic country, where anti-clericalism is sort of a family sport. What destroyed the Catholic Church in Spain was Vatican II, which destroyed the liturgy and devotions to which people were attached and also brought the religious orders to ruin. It was in fact the Catholic laity who revived and kept alive traditional Catholic practice with things like pilgrimages and processions, and who are currently leading the religious resurgence that Spain is experiencing in response to the attacks of the Zapatero government. Spain is much more Catholic than other Catholic countries, such as France or even Italy, and this is on the rise.
You might trying reading the work of Stanley Payne, IMHO the best, least partisan of the English language historians of Spain, if you would actually like to know something about both Spain and the Catholic Church in Spain in the years leading up to and following the war.
If one has no need for religion, they can ignore it, and go have a good time chasing women or whatever they like. No posse of clerics is going to go hunting for them. Any group of men that attacks a priest, or a nun, and burns a churches, are cowards, and enemies of good society.