The words fill my head
And fall to the floor
If God's on our side
He'll stop the next war.

For Bob Dylan, writing in the Sixties, the "next war" was the Big One - a nuclear exchange with the Soviet Union. His song "With God on Our Side" was taken to be a brilliant but routine protest number, satirising the Christian cold warriors in the US administration. But, as usual with Dylan, the obvious reading was the wrong one. The real target of his satire was not man but God. God hadn't stopped any previous war; there was, therefore, little prospect of Him stopping this one - the one that would destroy human civilisation. So, perhaps, He wasn't on our side after all.

It's a more than fair point. God and war have always sat uneasily together. In part, this is simply a way of expressing the problem of evil: if God is good and He made the world, how come it's so awful? God's children love war as much as their own children - or, rather, more, as they seem so eager to sacrifice their young on the battlefield. And war is getting worse, much worse.

Twentieth-century man, that uniquely vicious character, came up with the bright idea of the systematic targeting of civilian populations. Ninety per cent of casualties in conflicts in the first decade of the 20th century were military. In the 93 wars that killed 5.5 million people between 1990 and 1995, however, most of the casualties were non-combatants. In under 100 years, we had exactly reversed the equation of death.

All of which provides irrefutable evidence of the central Christian doctrine of original sin. As Aleksandr Solzhenitsyn said, the line between good and evil does not divide states; it divides the human heart. Germans didn't kill Jews because they were Germans, they killed them because they were human beings. It's what we do, given the chance.

Yet if original sin is justified by the facts, the rest of Christian doctrine would seem to be in ruins. The faith that proclaimed "God is love", "Love thy neighbour" and that His only begotten son died for our sins has done nothing to halt the carnage. In fact, for centuries, Christians have beaten ploughshares into swords with as much enthusiasm as anybody else. In the Garden of Gethsemane, Christ subdued his angry followers with the warning that those who live by the sword shall die by the sword. Later adherents seem to have misinterpreted this as a pretty good deal.

But now we have Rowan Williams, Archbishop of Canterbury, and Cormac Murphy-O'Connor, Archbishop of Westminster, condemning war with Iraq. It's what churchmen do these days. It's part of the ritual.

The other part is the hawks clutching their heads. The churches are out of touch, they say. Christians must go to war and, anyway, Dubbya is born again, so there. The hawk Mark Steyn, in the Sunday Telegraph, lost it completely. Writing of Williams's anti-war message, he concluded: "The archbishop offers only the certainty of decline, the final death-spiral into secular liberal irrelevance. No wonder Islam is Britain's fastest-growing religion."

This is what philosophers call a category error and hacks call missing the story. As it happens, I probably agree with Steyn that Williams has got it wrong about Iraq. But the error, the missed story, is in seeing Williams's intervention as just another liberal whinge, another death rattle from the established Church. For the new archbishop may well be the most significant figure to enter British public life in a generation, and what he said was not whingeing, it was the subtle voice of a type of Christian dissidence that was stifled 1,600 years ago by a deal with the Romans.

Williams is intelligent, very. On his appointment, one senior Catholic muttered to me: "At last, the Anglicans have got somebody smart enough to talk to our people in Rome." He is a brilliant theologian and a subtle and moving speaker. Intelligent people stopped going into politics 20 years ago - the present cabinet is clear evidence of that - but they kept on going into the Church. As a result, the average bishop, these days, is a good deal brighter and invariably better read than the average government minister. Williams is the climax of this process and if, as some have suggested, he is to become the leader of the de facto opposition, then Blairism is about to be trounced intellectually.

Williams's most important book is Arius: heresy and tradition. In the early fourth century, Arius denied the divinity of Christ - the doctrine is known as the Arian Heresy. Obviously, this was theologically momentous, but, less obviously, it was also of immense political significance. The political issue was the relationship of Christianity to the secular power. And that issue, in turn, hinged upon the central issue of Christian doctrine: what did the Crucifixion mean?

Who killed Christ? Was it God, man or the Devil? We say He died for our sins. But what does that mean? Plainly, we carried on sinning. We say His resurrection marked the defeat of death and the Devil. But we still die and evil still reigns. If you believe, these are urgent questions. But they should be just as urgent even if you don't. Christianity formed our culture and has underpinned the most powerful and successful civilisations the world has ever known. Understanding - or, at least, engaging with - its central dynamic is the only way we can hope to understand ourselves.

Seen purely as politics, the life and death of Christ was an attempted insurrection against Rome and the Jewish clergy. And for its first three centuries, Christianity was a dissident, underground cult. Then, with the conversion of Emperor Constantine, it began its rise to respectability. After the First Council of Constantinople in AD381, Emperor Theodosius officially established Christianity as the faith of the empire. The contract with the secular power was signed and justified by Christ's words: "Render unto Caesar . . ." Christianity, unlike Islam, accepted the necessary secularity of politics.

The great theologians of the Middle Ages - Anselm and Aquinas - formalised this state of affairs, and, in doing so, created the edifice of the modern Church. The Crucifixion was interpreted as an atonement that did not necessarily change things in this world, but certainly did so in the life to come. In spite of the gentleness of the teachings of Christ, Christians may still take up the sword in the name of the secular power or, as in the case of the Crusades, in the name of the faith itself.

Theologians of the modern era have tempered this with the concept of the just war - war as a necessary evil to combat injustice. Such a war is necessarily defensive and limited, and it must have clear, finite goals. But some have gone much further and questioned the whole contract with the secular power that permits Christian violence and the justifying theology. In this interpretation, the Crucifixion was not an atonement, in effect orchestrated by God; it was rather a demonstration of the stark contrast between the peaceful rule of God and the violence and death of the Devil's reign. True Christians must be pacifists.

This is an attempt to take Christianity back to the pre-Constantine faith. It carries particular weight in our time because of the clear similarity between Rome and America, both unchallengeable superpowers. It is also important because of the evidence of the failures of secular power. Not only do we still fight secular wars, but we also have secular poverty and starvation, as well as, in Britain, a total secular inability to construct effective public services. As I am sure Williams has seen, this may be the modern Church's big chance.

I don't know how far Williams goes with the idea of a pre-Constantinian faith. It is possible he will acquiesce in the disestablishment of the Church of England - establishment being our own peculiar, native version of the church-state deal. Whatever his final position, the Christmas message that so got up Mark Steyn's nose was a beautiful and timeless warning that should give even the most hawkish person pause.

Williams spoke of the Three Wise Men who told Herod of the birth of a king and thus triggered the massacre of innocents. They are, he said, like contemporary strategists who "miss the huge and obvious things and wreak yet more havoc and suffering". Williams knows what all wise men should know: that the one infallible truth about human beings is their incorrigible fallibility.

To be credible on Iraq, he must go further and come up with alternatives to force. Furthermore, does his awareness of our strategic incompetence mean we should never fight anybody, not even Hitler? But taken as a simple and poetic warning against imperial vanity, his message was as clear and true as anything that has been said on this subject.

Years after "With God on Our Side", an older and wiser Bob Dylan sang: "Strap yourself/To the tree with roots/You ain't goin' nowhere." That, probably, is the only answer to the earlier song's question. We don't know if God's on our side; we just know where we are obliged to stand. The Christian Church may be travelling back to an earlier, more dissident, more disestablished faith. And that may be a good thing. But, for the moment, the Christian civilisation that shelters you and me will still have to take up the proffered sword and defend the tree, roots and all.