This week HBO premiered Pussy Riot: A Punk Prayer, the documentary on the infamous Russian feminist art-punk group imprisoned for “hooliganism” after staging a protest in a Moscow Orthodox church. The film manages one surprise: almost all of those involved, on each side of the issue, come off more sympathetic than intended–except for Vladimir Putin, though in Putin’s brief appearance on screen he outwits a clearly uncomfortable British reporter.

With Putin as the villain, the girls are the intended heroines of the story, but the documentary does them a favor by humanizing them and spending much time with the girls’ families. Despite their juvenile politics, outsized egos, and at times strange choices of targets for their “art,” it becomes difficult not to at least admire their willingness to challenge an authoritarian regime that punishes dissent. Additionally, their jail sentences were far out of proportion to their crimes, their trial is rigged and unfair, and the state’s veiled threats to take away the young child of one of the girls is nothing less than inhumane. And yet despite the seeming simplicity of the stunts and the reactions they provoke, the controversy actually brings to the surface some complex and important questions about Russian society and the state.

In Conor O’Clery’s book on the last day of the Soviet Union, he writes of a Moscow Catholic church service attended by 82-year-old Yulia Massarskaya, who has come to her first such service since she was eight years old when the 1917 October Revolution took place. “I have never felt this good,” Massarskaya says. “It is like coming back home.”

Massarskaya was far from alone. There is a scene in A Punk Prayer of a pro-Orthodox protest, in which we hear from those the girls offended–among them women old enough to have lived through decades of Soviet religious repression. “For 70 years, we couldn’t practice,” one of them says. “We drank our faith in with our mother’s milk. For us, this place is sacred. In 1812, people collected coins to build it. And look what they’ve done.” The documentary, to its credit, then reviews the anti-religious policies instituted after the Bolshevik revolution.

That is not to excuse the punishing of “blasphemy”–something the Russian state will do explicitly when two new laws take effect next month. Indeed, outside of the United States the spread of such thought police is truly depressing, especially in Canada and the European Union, which should know better. It is simply to point out that many of those offended by the Riot girls are far from Putinists; some of them make it clear they don’t want the girls spending years behind bars but are pained to have been targeted by the state for virtually their entire lives and now feel targeted by so-called liberals in Moscow. They, the believers would like the girls to acknowledge, are not the enemy.

But that brings us to the most destructive part of the girls’ show trial and imprisonment, and it is easily the most misunderstood aspect to the controversy. Putin is not meting out such punishment to defend or to glorify the church. He is taking a wrecking ball to the church once again, even if only metaphorically. By tying the Russian Orthodox Church to his regime’s repression, he is ruining it in the public consciousness.

Khrushchev promised to “take God by the beard”; Putin wants to enlist God in his crimes and his politics. Communists sought to erase and replace God; Putin wants you to think of God as his prime minister. In A Long Walk to Church, Nathaniel Davis’s essential study of religion in Russia, the author explains the root and logic of the Communists’ assault on the church:

Think of a “City of God” in the Soviet Union, which the communists assaulted in their days of militant atheism. The city’s “temples” might represent the various religious bodies, each one rooted in the earth, where the city could be attacked and where its dimensions on the ground could be measured. Each of the temples also had–and has–a vertical dimension in the realm of the spirit, and no one who stood on the earth could clearly see to the tops of the columns, domes, and towers, as they were shrouded in mist. That is the realm of philosophers and theologians, who are not earthbound. This study will describe the situation on the ground; it is at this level that the communists made their assault, because they too were earthbound. …

The image of an earthbound “temple” is intended only to distinguish the inquiries of the historian and the philosopher, not to describe the churches as inert or the historian’s task as a simple measurement of dimensions and unchanging forms. At its heart a church consists of people; it might better be described as “an army on the march.”

And that army had to be defeated by the conquering power. But it turns out there were two obstacles standing in the Communists’ way: first, that an army of God is not so easily defeated or demoralized; and second, sometimes it is more convenient to allow its uneasy coexistence with the state. Soviet leaders soon figured out an ingenious way to fight both the earthbound manifestations of the church and its spiritual sustenance: infiltrate and co-opt it.

The rest is history, and it explains why Russians felt they were “coming back home” when the Soviet Union fell and they returned to church. They were permitted to practice before the dissolution of the empire, but there was something impure about the church’s unholy alliance with the state. The controversy over Pussy Riot is so difficult for Russia’s Christian believers precisely because Putin is co-opting their church once again.

The Riot girls fanned such flames, but in the minds of the Orthodox the girls were not blameless either. Their atheistic attack reminded churchgoers of the Red atheism that destroyed the church in their youth. It’s not for nothing that in A Punk Prayer one Riot girl’s father tells us that “until the age of four, Nadia was raised by her grandmother, who was a strong-willed Communist, and maybe that’s why we brought up such a little Bolshevik.”

Russia’s Orthodox thus feel under attack from all sides. The Riot girls self-consciously target “conformists,” but do not come off as openly hostile to religion itself. And they will not bring down the church, nor commit acts of violence against its adherents. At the same time, we can understand why this is such a touchy subject for everyone involved. The wound is not yet healed, and Putin intends to keep it that way.