Benedict, as his friend and associate noted, is sincerely committed to dialogue between Christians and Muslims, but he also believes that the link between terrorist violence and its sponsorship by some Muslim clerics is a big obstacle to further progress.
His reaction to 11 September gave a first hint of his view. 'It is important not to attribute simplistically what happened to Islam. It would be a great error', he told Vatican Radio. But that did not prevent him from asserting immediately afterwards that 'the history of Islam also contains a tendency to violence'.
There were two strands, he added: the other being a 'real openness to the will of God'. 'It is thus important to help the positive line, which does exist in its history, to prevail and to have sufficient strength to win out over the other tendency.'
There might have been less protest had Benedict a clearer record in favour of dialogue with Islam. As a cardinal in the Holy See, he was known to be sceptical of John Paul II's pursuit of conversation. One of his earliest decisions as pope was to move archbishop Michael Fitzgerald, one of the Catholic Church's leading experts on Islam, and head of its council on interreligious dialogue, away from the centre of influence in Rome, and send him to Egypt as papal nuncio. Benedict has spoken publicly of Christianity as the cornerstone of Europe and against the admission of Turkey into the EU. But he has also accepted an invitation from Turkey's president to make the first-ever papal visit in November. That visit, which could have been a symbol of his commitment to the reconciliation and respect between religions of which he has also spoken, may now be at risk. The Pope has lived a cloistered life, rarely exposed to the unholy nuances of world politics. He needs advisers around him who are. However, the Vatican has apologised. That should be enough for what was almost certainly nothing more than an ill-judged remark. For there is a second strand to this argument. There cannot be dialogue without rigor and openness. The Muslim world should also take pains to be thoughtful in its response, and perhaps less quick to take offence.
Damian Thompson of the Telegraph comes through with two good pieces, yesterday and today.
It is ironic that Benedict XVI finds himself accused of crude anti-Islamic prejudice after quoting a medieval emperor's opinion that Mohammed's violent teachings were "evil and inhuman".
For no pope in history has made a deeper study of Islam. Having explored every verse of the Koran, and engaged in long debates with Muslim scholars, he rejects the simplistic notion — held by fundamentalist Christians, and by the Roman Catholic Church until the middle of the 20th century — that Islam is evil. Yet he is convinced that some of its doctrines are morally indefensible.
In Benedict's view, a profound ambiguity about violence lies at the heart of Islam, arising from the Prophet's belief that faith can be spread by the sword. Mohammed, after all, was a general whose troops beheaded hundreds of enemy captives.
Asked recently whether he considered Islam to be a religion of peace, the Pope replied: "Islam contains elements that are in favour of peace, just as it contains other elements." Christianity, by contrast, he sees as a religion of pure peace — which is why he adopts a near-pacifist approach to conflict in the Middle East.
Where the pontiff differs from his predecessor is in his impatience with what might be termed "Islamic political correctness".
John Paul II hoped that prayer could bring Christians and Muslims closer together, and famously prayed alongside Islamic leaders at Assisi in 1986. He also reassured Muslims that "we believe in the same God".
Benedict would emphasise that the Islamic understanding of God is radically different from that of Christians.
He has also refrained from issuing the apologies for historical misdeeds made by John Paul II, arguing that they are never reciprocated.
The Pope's professions of "respect and esteem" for Muslims are not new: as the Vatican's doctrinal watchdog under John Paul II, he fully supported the attempt to find theological and cultural common ground with Islam.
But he is more pessimistic than his predecessor and has not followed John Paul's example of issuing blanket apologies for Christian crimes in the distant past, believing that they only fuel resentment. He supports dialogue, but more as a means of heading off conflict than of making any theological breakthrough.
Conspicuously missing from yesterday's statement was any apology for Benedict's discussion of the relationship between Islamic teaching and violence.
The Pope believes that the concept of holy war is both integral to Islam and morally wrong — and this weekend's furious row will not alter his opinion one iota.
Indeed, he would rather call off his forthcoming trip to Turkey than reiterate the platitudes of Christian liberals who present Islam as an entirely peaceful creed.
If anything, the attitude of the Pope and many Catholics will have been hardened by what they regard as a deliberate attempt to cause trouble by Islamic spokesmen — and by the media. The BBC, in particular, has appeared to give undue space to the views of extremists.
In the end, the Vatican response can be summarised as follows: the Holy Father may have walked into an avoidable trap but the real villains of the piece are agitators and journalists who have maliciously twisted his words.
In fact, the speech itself suggested that the Pope understood perfectly well that there are nuances to the Islamic idea of jihad. He cites an early verse in the Koran that "there is no compulsion in religion". And in respect of the verses that exhort Muslims to take up arms for the faith – and no, we're not talking merely about a spiritual struggle, but the real thing – he notes that there are differences between Mohammed's treatment of Christians and Jews, and of pagans.
If you're looking for a real critique of Islam in the speech, there is one tucked away in the text, but hardly anyone noticed. The Pope suggests that the Islamic idea of God is so transcendent that he cannot be seen in terms of human reason. He cites one medieval Islamic scholar, Ibn Hazn, who says that God is entirely remote from our rational categories.
This may not sound like much to get worked up about, but Benedict plainly sees this approach as the opposite of the Christian way of looking at faith and reason. And indeed, a Rome-based Muslim theologian, Adnane Mokrani, has pointed out that this is only one Islamic view of God's nature, and other schools of Muslim thought are very different. Now that's proper religious dialogue.
As for the Pope's notional Islamophobia, he's had rather a good record until now in terms of the issues that agitate Muslims. He was sympathetic to their reaction to the Danish cartoons, and he was strongly opposed to the conflict in Lebanon and the war in Iraq.
The irony of this row is that it is the opposite of what the Pope was trying to achieve. Benedict ended his speech by hoping for a new dialogue between the sciences, religions and cultures "which is so urgently needed today". It looks, from this miserable episode, as if you can only have a conversation that deals – however remotely – with Islam on Muslim terms. Not much of a dialogue, then.