Had Pope Benedict XVI omitted the citation of Emperor Manuel II Paleologus's remarks about Prophet Muhammad bringing only what is "evil and inhuman" to the world, a quote he himself admits was "marginal" to his argument, then he would have focused attention on his real offence in that scholarly talk: his shoddy scholarship on Islam.
He would have also permitted a more healthy focus on his central argument, that modern secular rationalism needs to heed the contribution of faith to enable it to break out of the narrow confines of positivism and empiricism.
The skeleton of the pope's argument can be summed up in the following syllogism: Islam is faith devoid of reason; modern secularism is reason devoid of faith; Christianity is a dynamic wedding of faith to reason.
Both faith without reason and reason without faith can be very destructive. Ergo, both Islam and modern secularism should learn from Christianity the art of the mutual enrichment between faith and reason.
This line of argument has as many holes in it as a chunk of Swiss cheese, starting with the substandard scholarship on Islam, in which the archaic, careless and insensitive quote was not the most serious lapse.
"I humbly appeal to all fellow Muslims to embrace intellectual discourse and constructive criticism with non-Muslims or even between Muslims from different sects (Sunni, Shia, etc), so we can live in peace."
Bubacarr Sankanu, Germany
This said, however, the phenomenal overreaction of Muslim leaders and masses around the world to the pope's remarks may prove that we as Muslims do indeed have a problem with rationality.
Most of those who reacted have certainly not read the pope's speech in full, and, even if they had, the proper response should not have been demonstrations on the street and salvos fired at political rallies, but scholarly rebuttal and calls for dialogue.
No purpose is served by stirring anger among the masses who should have no input in such an exchange, and who are certainly responding to what their leaders are telling them about the remarks and what they signify.
There is no doubt that remarks made by the head of a religious community carry more weight than remarks made by lesser mortals, and this puts a great responsibility on leaders to choose their words carefully.
There is also no doubt that the pope was wrong, not only about both Muslim theology and history, but also about modern realities.
His central point of connecting Islam and violence appears to imply that the main problem of our time is the presence of Muslim armies at the gates of Europe poised to spread Islam by force.
If the pope wanted examples of forced religious conversions, he should have cited those, or the more recent colonial expansion which brought Christianity (and genocide) to many parts of the world at gunpoint
Not even Osama bin Laden is making such claims. The Palestinian, Lebanese or Chechen jihadists of today are not indicating a desire to spread Islam, but national territory.
If there are armies on the loose today claiming to spread something, it is the Western (Christian?) armies in Iraq and Afghanistan, claiming to spread democracy.
The pope's remarks, if they are to be relevant, should have been directed to that endeavour, not to presumed medieval invasions.
He happens to be wrong on the medieval part as well.
The Turks did not act to spread Islam by force when they occupied parts of Europe. In fact, the recurring crises in the Balkans have their roots in the fact that the Turks did not practice the same ruthless ethnic and religious cleansing the pope's co-religionists had practiced during the same period he had referred to in Sicily, Portugal and Spain.
If the pope wanted examples of forced religious conversions, he should have cited those, or the more recent colonial expansion which brought Christianity (and genocide) to many parts of the world at gunpoint. There is no record in history of forced conversions to Islam anywhere in the world.
The pope's remarks about the banishment of reason from Islamic theology are also mistaken and, for a former theology professor, astonishing.
The rarefied theoretical reflections of professional theologians about whether God has the right to commit injustice and do evil things are beside the point, referring as they do to mere hypothetical situations.
They do not reflect on what God has actually told us he would do, and they are certainly irrelevant to what is demanded of human beings, who are not supposed to have God's status.
In citing the ideas ascribed to to the 11th-century Andalusian theologian Ibn Hazm, the pope projects the false impression that his were mainstream views within Islam. This is done by omitting even to mention the man's full name, Ibn Hazm al-Zahiri (the Literalist), a reference to the "literalist" school of thought to which he belonged, and which has no adherents among Muslims anywhere today, and had never had a substantial following anyway. Ibn Hazm was celebrated more as a literary figure than as a theologian.
In contrast to mere speculation, the texts are quite categorical about God's rationality, mercy and justice.
The protection of reason is the second of the five basic principles accepted by Muslim theologians as the central objectives of revelation, coming after the protection of faith and before the protection of life
The Just, Wise, Merciful are so central to the Muslim conception of God that they are counted among God's Holy Names.
The texts categorically make it clear that God does not act irrationally or unjustly.
These points are not disputed even by those who speculate that God could have indeed chosen to act otherwise. And in any case, even those who indulge in such ruminations do not accept that human beings are allowed to commit evil or act irrationally.
The protection of reason is the second of the five basic principles accepted by Muslim theologians as the central objectives of revelation, coming after the protection of faith and before the protection of life.
Of more interest to Muslims and others is the pope's spirited defence of the "European-ness" of Christianity. It was extraordinary for the reputedly traditionalist leader of the traditionally conservative Catholic Church to spring to the defence of the Greek input into Christian doctrine (which admits had a distorting impact on the original Christian message) and dismiss the calls of those who want to reassert Christ's original message through de-Hellenisation.
This stance sheds important light on his defence of Europe's Christian identity, which he had argued should exclude Turkey. For here, we find him actually defending Europe against any attempt to re-link it to Christianity's roots in the East.
This is as remarkable as his apparent exclusive linking of rationality to Greek thought, as if the rest of humanity had no access to rationality independent of Greek texts. It would appear here that it is European exclusivity he is defending, rather than Christianity.
But this leaves his Holiness with a slight problem: Most of what he describes as Greek rational thought has originated in today's Turkey.
This said, however, the vociferous and intemperate reactions among Muslims to the pope's remarks remain ill advised and do more harm than good to the already damaged image of Muslims worldwide.
The skeleton of the pope's argument can be summed up in the following syllogism: Islam is faith devoid of reason; modern secularism is reason devoid of faith; Christianity is a dynamic wedding of faith to reason
In order to prove the pope wrong (a rather difficult proposition, given that he is infallible) Muslims should react to his remarks in a rational and measured way. His speech should be studied by specialists and responded to calmly on the intellectual level.
More important, it is necessary to rebuild the proper Muslim civil institutions which could have both the capability and authority to respond effectively and in a measured way to challenges facing Muslims today.
Like terrorism, the spontaneous (and sometimes orchestrated) reactions to perceived attacks on Islam reflect the general inadequacy of the state and civil organisations, which lack both the authority and the effectiveness in dealing with the perceived challenges.
In less dysfunctional systems, violence should be the monopoly of the state, while speaking on religious issues should be the function of competent authorities.
The fact that these issues are dealt with by people on the streets is an indication of a very serious pathology that needs to be remedied as a matter of urgency.
Dr Abdelwahab El-Affendi is a senior research fellow and co-ordinator of the Islam and Democracy Programme at the Centre for the Study for Democracy, University of Westminster, London.
The opinions expressed here are the author's and do not necessarily reflect the editorial position or have the endorsement of Aljazeera.