There is something oddly Shakespearian about the story of Pussy Riot, the Russian feminist punk-rock collective staging impromptu events in balaclavas. It recalls the narrative of King Lear's Fool – the laughter dying, the farce drawing to a mysterious, possibly violent close. It likewise recalls the story of the Jester in Andrei Tarkovsky's Andrei Rublev, a shimmering, brutal portrait of 15th century Russia. The Jester is obscene and irreverent, mocking both the state and the church – and suffers an unenviable fate.

Three alleged members of Pussy Riot – Nadezhda Tolokonnikova, Maria Alyokhina, and Yekaterina Samusevich – were jailed after they performed a "punk prayer service" at Christ the Saviour cathedral in downtown Moscow. The masked women ran to the pulpit and sang a song asking the Virgin to "chase [Vladimir Putin] away," repeatedly crying "holy shit", dropping to the floor and crossing themselves. They were swiftly escorted out. Arrests soon followed.

I felt pain when I saw the YouTube video dedicated to the performance. I'm not a good Orthodox Christian girl by any stretch of the imagination, but the church, to me, is still sacred – even a church such as the Cathedral of Christ the Saviour. Destroyed by the Bolsheviks, the cathedral was rebuilt to play an odd role in Russia's spiritual life – it showcased the worst of what the newly powerful Orthodox church had to offer: pomp, circumstance, and tasteless frescoes. I wish that it had been spared Pussy Riot's punk prayer service.

But my hurt at what had occurred was swiftly replaced by horror. It was as if the extremists among Russia's Orthodox Christians were lying in wait for the opportunity presented by Pussy Riot. There were calls to shoot the women. To burn them alive. To strip two of them of their parental right. Pussy Riot supporters were punched at rallies, people with T-shirts saying "Orthodoxy or death" held court on the news. The protest movement, meanwhile, was divided and confused. Christian members of the opposition faced accusations of colluding with the enemy in the face of the church. Those Christians who openly called for mercy and leniency were hounded by their more reactionary counterparts. Someone threatened the judge who allowed Pussy Riot to remain jailed ahead of trial with an axe. It was a mess. It still is.

Worst of all, Pussy Riot's fate now lies in the hands of Russia's criminal court system. As a frequent observer of these courts, I cannot help but point out that they are terrifying. In Moscow alone, over 90% of all criminal court cases end up in convictions; anything less would threaten the close relationship of the courts and the prosecutors. Whenever fellow believers say that "the courts should decide" what to do with Pussy Riot, they are either being naive or openly contemptuous. The courts are there to blindly, brutally enforce the social hierarchy, just like they did in Soviet times – not to get to the bottom of controversial criminal cases.

The incident and its aftermath made apparent the severe dissonance between my actual faith and faith as it is publicly practised and I, a grown woman, found myself crying over this. The dissonance is so enormous that it hurts me – it makes me feel weak, cowardly and helpless. As Orthodox blogger Artyom Tasalov put it: "More than ever now, I am convinced that what [Pussy Riot] did was allowed by God, so that our hearts' intentions were revealed. How much darkness and purulence do our hearts contain."

The pain flared up again this week, when the preliminary investigation against Pussy Riot was completed. They face charges of hooliganism motivated by religious hatred (decried as baseless by their lawyers) and may face seven years in prison. In many ways, the women of Pussy Riot now appear to be scapegoats at a time of political crisis in Russia.

Russian author Dmitry Bykov dedicated a poem to the arrest of Pussy Riot:

"I'm not a fan of the rioting pussies, of their group prayer

I'm not a friend of the punks either – may they forgive my boring tastes.

But why not forgive this stupidity, to excuse this buffoonery?

(I'm trying to sound as toothless as possible, so as to not anger anyone)."

At a time like this, would Jesus have retreated into the comfortable opulence of the church's administrative offices? Or would he have gone knocking on the jailhouse doors? I don't need to think hard about the answer.

• Follow Comment is Free on Twitter @commentisfree