Three 20-something women who look, in their glass courtroom cage, no more than girls, are being tried in Moscow for "hooliganism". The charge, which could see them imprisoned for seven years, relates to an anti-Putin song they sang in Moscow's main cathedral. The case of the Pussy Riot three has, rightly, prompted outrage, both that criminal charges were brought at all in response to what appears little more than a punk-band prank, and for the harshness of their treatment – they have spent the past five months in custody. The celebrated quotation about "a butterfly broken on a wheel", which headed a Times editorial about Mick Jagger's 1967 drugs trial, has received a new outing in the English-speaking world.

Amid the outrage, however, one aspect of the case risks being lost. In performing their anti-Putin routine before the altar of the cathedral of Christ the Saviour, the women offended not just one, but two, powerful constituencies. The first, and the one most Western condemnation has focused on, is Vladimir Putin – back in the Kremlin for a third presidential term. But the second is the Russian Orthodox Church.

It is a little as though British anarchists had called for the Queen's head from the altar in Westminster Abbey, in an age when both the monarchy and the Church were held in awe. Even this comparison, though, underplays the position of Russia's Orthodox Church.

For all the compromises with secular power that taint its past, the Church is one of very few institutions that have flourished since the fall of the Soviet Union. Gorbachev's perestroika relaxed the grip of official atheism, and churches rushed to re-gild their domes and commission new icons. Orthodoxy became a rallying point for Russians' reclaimed national identity.

And the cathedral of Christ the Saviour has resonance beyond this. Built to commemorate the retreat of Napoleon and dynamited by Stalin, it was rebuilt on the personal order of Russia's first post-Soviet leader, Boris Yeltsin. The crowds that now throng its services testify to the religious, as well as national, revival of the past 20 years.

Some of the fiercest ire against Pussy Riot has come not from the Kremlin, nor from a patently equivocal Prime Minister, but from Orthodox clergy and ordinary people, who regard the group's antics as blasphemy, and do not separate Church and State. The Kremlin's hand may indeed be discerned in this prosecution, but so can the outlines of a dispute about tolerance and what sort of society Russia wants to be. The reference to "breaking a butterfly on a wheel" is thus still more pertinent than it might seem. The Pussy Riot trial is about culture quite as much as it is about power.

m.dejevsky@independent.co.uk