More than a decade and a half ago, I travelled to Holland to meet – in the anonymity of a train station café at Leiden, at his request – one of the most brilliant Arab professors of Islamic thought, Nasr Hamid Abu Zeid.

This rotund, friendly, secular man had been declared an apostate by a Cairo court, deprived of his university professorship, and shamelessly hounded out of Mubarak's Egypt in 1995 after an official declaration that he was now divorced from his wife, Ibtisam Younis. As an apostate, how could he have a Muslim wife? Ibtisam, a professor of French, followed her husband into Dutch exile.

Nasr Abu Zeid's sin was his belief that the Koran must be subject to reinterpretation, that centuries of Islamic scholarship needed to be re-studied. And this is what he said to me in that Leiden train station café in 1996: "If you consider the situation in the Muslim world, the absolute absence of political freedom and the failure of all the projects which were started by socialism, communism, nationalism – absolute failure – the poor Muslim citizen finally got nothing. And he was deprived even of his liberty to think – 40 years with the absolute absence of democracy, of liberty! Only one voice was allowed. We had to echo the voice: the president, the king, whatever. Obedience to the ruler became some sort of religious conviction. So obedience here is the key word."

Abu Zeid was a tough guy who didn't conceal his anger at the outrageous way in which he had been treated. "In the plane, I was very angry. And I told my wife: 'If I die in any place – in Holland, in Spain – just bury my body where I die. Don't think about taking my body back to Egypt ... at the end, all the lands – it's the earth of God!" Here was a 20th-century – indeed, a 21st-century Muslim – reflecting on a retrograde, accusatory Islamist "renaissance" that was opposed to the Western Renaissance. "Here it comes," he told me. "The Islamicisation of knowledge – instead of the modernisation of Islamic thought!"

Those were dangerous days. The Egyptian novelist Naguib Mahfouz was stabbed in the back, an Egyptian academic, Ahmed Mansour, imprisoned for six months because he had supposedly rejected a tenet of Islam in researching the Prophet Mohamed's hadith – the "sayings" of the Prophet, set down many years after his death and quite different from the text of the Koran. Courts – often alerted by the stupidest of prelates – threatened journalists and singers as far away as Lebanon.

But today? Surely the doors of Islamic perception may now swing open in the Arab world. It's not for Westerners like me to say so. But I ask it after reading Tom Holland's stunning new blockbuster In the Shadow of the Sword, in which late Romans fight the Persians and leave open the wreckage of both superpowers to the advance of Islam. Forty years ago, Holland writes, two German scholars were allowed by the Yemeni government to examine a cache of ancient Korans found in the ceiling of Sanaa's oldest mosque, stuffed into hessian sacks, fragments of probably the oldest Korans in the world. One of the Germans concluded that the Koran – like the Bible – had evolved over time and was a "cocktail of texts".

You can guess what happened next. Outraged Yemenis ran for cover, and the Koran fragments have remained unpublished, unseen, stashed away in secret ever since. The problem, needless to say, is that popular tradition has it that there is only one Koranic text, that it contains the words of God himself, that those words – and only those words – are the recitation ("koran") of God to Mohamed. End of story. The Caliph Othman, the Prophet's fifth cousin once removed (and married to two of the Mohamed's daughters) decided that there should be only one definitive text of the Koran. His scholars chucked out all unauthenticated texts and put together the genuine version, albeit that the suras – or chapters – were arranged by length rather than chronologically. Yet in the 10th century, Ibn Mujahid decided that there were seven equally valid readings of the Koran.

But here's the point. Holland goes on to compare Islam with other religions, talks about the references to Jesus in Islamic texts – Palestinian professor Tarif Khalidi, who has just produced a magnificent new translation of the Koran, wrote extensively about Jesus in Islam – and also tries to date the Koran (scarcely referred to for 200 years after the Prophet's death) to the actual time of Mohamed's life. And he pretty much comes to the conclusion that the Koran was indeed contemporary. There is one reference to the Romans in the Koran, and Holland convincingly suggests that the passage containing a report that "the Romans ... have been defeated in a nearby land, and yet, after their defeat, they shall be victorious..." (Koran 30:1) refers to the Persian Khusro II's victory over Byzantine Rome in Palestine. This is great stuff, religion and history as one, belief supported by facts – very much like the Roman Pliny's disinterested account of how he executed Christians who refused to deny their faith.

We are supposed to be treading on eggshells here. One of Holland's reviewers mentioned the Islamists who have taken umbrage at such research. "We must hope that Holland is spared their wrath," he intones. But this is preposterous. Holland confirms that Mohamed was a real man and the more the Prophet is real – and the more Christ is real, for that matter – the more compassionate should a monotheistic God's followers be. Islamic Awakening, then?