Robert Fisk: Even the little dog was not spared by Cromwell

To Saint Canice's, then, in the ancient city of Kilkenny, its ninth-century round tower still watching for Viking invaders, home of the forgotten Gaelic Irish-Old English Confederation, its citizens spared by Cromwell.

And there in the nave are the tombs of John, Second Marquess of Ormonde, Margaret and Piers Butler and Richard Butler and Margaret Fitzgerald, righteous beneath their effigies. Larkin could have composed his verses here.

Side by side, their faces blurred,

The earl and countess lie in stone

Their proper habits vaguely shown

As jointed armour, stiffened pleat,

And that faint hint of the absurd –

The little dogs under their feet

Yet as I pad beneath the vaulted wooden ceiling and run my hands over these stone effigies, I realise that they have no faces, just rough gashes which have sliced off their noses and ears and eyes. The 17th-century English Taliban, with their axes and swords, were at work here, hacking away the images of the knights of Ireland. Angry Cromwell's New Model Army must have been, for one poor knight has not only lost his face. An English soldier, way back in 1650, plunged a pike or a dagger into the man's codpiece and then – here comes the sign of fury – attacked that faint hint of the absurd. The little dog upon which the knight's feet rest has been beheaded.

Fresh from the slaughter at Drogheda, Cromwell would spare the citizens of Kilkenny, but not its Cathedral of Saint Canice whose stonemasons packed their bags in 1285. Cromwell smashed the stained glass windows, stole the bells, threw the baptismal font to the ground and turned the cathedral into a stables. His soldiers broke open the tombs and hurled the bones of their lords and ladies into a pit in the churchyard. The half-Irish writer Constantine Fitzgibbon noted almost 40 years ago: "If Cromwell and his people had possessed the technical ability to build gas chambers and drop Zyklon B upon the Irish Roman Catholic subhumans ... they would undoubtedly have used such methods."

So much, then, for the Great Rebellion of 1641. So much for the king's men. The New Model Army was the first ideological battle group since the Crusaders. Why, had not the Parliament of England passed a decree for the absolute suppression of the Catholic religion in Ireland? Traitors and infidels. Smash their graven images. Smash the Buddhas of Bamian, for that matter. The real Taliban used explosives. Cromwell's armed puritans used the sword. No dancing. No music. No films or television or kite-flying. Read the Bible – only the Bible. Read the Koran – only the Koran. What's the difference? Cromwell and Mullah Omar did everything in the name of God.

Thus did I reflect as – in those slightly grim moments that always precede a lecture – I prepared to bore a cathedral audience of hundreds with my usual paint pots. Treachery in the Middle East, Iraqi slaughter, Afghan bloodbaths, the connivance of governments and journalists, the lies inherent in our words of war, the need for our military – with their guns and tanks and Apache helicopters – to leave the Muslim lands.

Yet just to my right as I spoke lay a plaque of white marble, the memorial tablet of one General Sir Arthur Pack (of this parish, of course) who fought and was wounded at Sevastopol in the Crimean War. Unwounded at Sevastopol was Lawrence Knox, another Irishman who would go on to found The Irish Times. Knox had even ridden over to the site of the preposterous charge of the Light Brigade and wrote in his diary on 31 May 1854 that there were "still numerous skeletons of horses laying about and one skeleton of a man in the 11th Hussars who still had on his red cherry-coloured trousers and was laying on his back ... So I suppose he lay down there and died".

In the Crimea, we were fighting the Russians. On our side were France and Sardinia and – Turkey. The charge of the Light Brigade, Sevastopol, was fought with Muslims as our allies. We were trying to stop Russia encroaching on the Ottoman empire – which just over 60 years later would be genociding the Armenian Christians and fighting us. Come to think of it, Knox did later come across "a young woman ... laying on a sofa with her throat cut and it was supposed to have been done by the Turks".

So there I was, giving the Hubert Butler Lecture – he being a distant descendant of the Butlers in those plundered tombs, a journalist, writer and historian with an Anglo-Irishman's "savage indignation" to rival that of Jonathan Swift. After helping to save the Jews of Austria from the Nazis, he spent years investigating the life of Archbishop Aloysius Stepinac, the vicious Catholic prelate – friend of the wartime Nazi surrogate in Croatia, Ante Pavelic – who spent four years campaigning for the forcible conversion of Orthodox Serbs. (The alternative was to have your head sawn off by the Ustashe murderers at Jasenovac extermination camp.) Butler discovered that Pavelic's even more outrageous interior minister, Andrija Artukovic, had spent a pleasant post-war year in Ireland, under an assumed name and with the help, of course, of the Catholic Church.

But his revelations about Stepinac earned Butler the Cromwell-like hatred of the same Catholic Church in Ireland. He was pilloried in the press and insulted by the Papal Nuncio. Kilkenny County Council expelled Butler from one of its subcommittees and he was forced to give up the honourary secretaryship of a local archaeological society which he himself had founded. Taliban purity was what he lacked.

At the post-lecture Kilkenny Festival dinner, some of us debated the desire to be intolerant, to smash tombs and graven images and Muslims – first we fought for them, then we fought against them – and destroy the happiness of men like Butler. I blamed God. And so to bed.