So he got religion — or at least pretended to — and made an alliance with the Russian Orthodox Church. That's why he is now warning that there may be bloodshed if the Ukrainian Orthodox Church is allowed to break away from the Moscow patriarchate.
The president of Russia got the best education the Soviet state could provide, and his private opinion about the Russian Orthodox Church is probably not far from that of Pussy Riot (although they would agree on little else).
But the Church has always served the interests of the Russian state if it is allowed to, and — as the embodiment of the Russian state — Putin feels obliged to return the favour.
What has upset Patriarch Kirill and his colleagues is that last weekend Ecumenical Patriarch Bartholomew of Constantinople granted a "tomos of autocephaly" to Metropolitan Epiphanius of the newly formed Orthodox Church of Ukraine. Which probably needs a bit of translation.
The Ecumenical Patriarch is the head — or rather, the "first among equals" — among the heads of the various national Orthodox Christian churches. Constantinople, actually now Istanbul, is still the headquarters of Orthodox Christianity although it has been under Muslim control for over 500 years.
The Ukrainians had asked Patriarch Bartholomew if they could have their own church back and, after due consideration, he decided that they could. The tomos of autocephaly (independence) was the document that contained his decision ... he was just putting things back the way they were.
Kiev, now the capital of Ukraine, was the first capital of the Russian state and naturally the headquarters of the Russian Orthodox Church as well. But Kiev was destroyed in the Mongol invasion of 1240, and for centuries afterwards the new centres of Russian civilisation were in the forests far to the north.
In 1686, when Muslim slave-raiders from Crimea were still operating regularly in the vicinity of Kiev, the patriarch in Constantinople officially transferred the seat of the Russian Orthodox Church from Kiev to Moscow. All that's really happening now is that Kiev is getting its own patriarch back.
The people who live in this area now are called Ukrainians, speaking a language somewhat different from Russian. Normal Orthodox rules say that each national group is entitled to its own national church, so what's the problem? Politics, of course.
For three centuries after 1686, Ukraine was part of the Russia empire and its successor, the Soviet Union.
It was the Russian Orthodox Church that made the religious decisions for everybody, and received the revenues from the 12,000 Orthodox parishes in Ukraine. But since Ukrainian independence in 1991, all that has been in question.
The question became more urgent with Russia's unilateral annexation of Crimea in 2014 and its military support for separatists in eastern Ukraine since then. Moscow wanted to keep control of the Orthodox Church in Ukraine, since it was a way to influence Ukrainian opinion in Russia's favour — but, for the same reason, it was a priority for Ukrainian nationalists to expel the Russian influence.
Ukraine won, and Ukraine's president, Petro Poroshenko, thanked Patriarch Bartholomew last weekend "for the courage to make this historic decision ... Finally, God sent us the Orthodox Church of Ukraine."
(Is Poroshenko really a believer? Maybe, but he's certainly running for re-election in March.)
Putin and Poroshenko are both using religion for their own purposes, but Bartholomew just did what was right. That has a cost: the Russian Orthodox Church accounts for almost half of the 300 million Orthodox Christians in the world, and the hierarchy in Moscow has now broken off relations with the patriarchate in Constantinople.
This is a schism that may take a long time to heal.
But Pussy Riot should have the final word. As they said in their famous "punk prayer" in the Cathedral of Christ the Saviour in Moscow in 2012 (for which two of them did serious jail time):
The Church praises rotten leaders, The march of the cross consists of black limousines Patriarch Kirill believes in Putin, Would be better, the bastard, if he believed in God! Virgin birth-Giver of God, drive away Putin! Drive away Putin, drive away Putin!
Gwynne Dyer's new book is Growing Pains: The Future of Democracy (and Work).