To be quite sure, the quote of the 14.Century Emperor, which Pope Benedict used to explain his point that God works through reason was tactically not well chosen.
And yes it could lead to misunderstandings.
But if one reads the whole lecture one can be assured that it was in no way meant as a part of a "clash of civilizations".
One also has to realize in what context the lecture stood and who the audience were.
It was meant for university students and professors, most of them non-religious people in a place were reason is of the utmost importance. Many of them were probably people, who could not conceive that reason and religion could have some common ground.
Pope Benedict used to be a Professor of Theology and when he held the lecture he fell back into this role. For an academic in theology or philosophy words and quotes are not used in a tactical manner but as an invitation to analysis and dialogue.
This invitation to dialogue is what Pope Benedict mentioned in his apology towards the Muslim people. And there were Muslim theologians who understood it in exactly this way.
The whole lecture was meant as reasoning that faith in God was NOT unreasonable.
The Pope compares the early theology of the Church which was influenced by Hellenistic reason to the teachings of a certain Islamic theologian.
The New Testament written in a Greek environment was influenced in its wording by this environment, like the beginning of the Gospel of John: "In the beginning was the Word and the Word was with God and God was the Word." The Greek word "logos" or "word" has also the meaning of "reason" and "logic".
So the early Church believed that God worked through reason, but according to the French scholar of Islamic religion R. Arnaldez the Islamic theologian Ibn Hazm believed that God transcends even reason and logic.
So this 13.century Emperor declared that the use of violence to spread faith was against God's reason.
And then Pope Benedict explains that in the middle ages Christian theology have strayed from these believes of reason and had become very close to the opinions of Ibn Hazm, believing that we would only know the ordained will of God, and beyond this was God's freedom where he could have done exactly the opposite of what He has done. But mostly the Church has kept to the belief that there is an analogy between the Spirit of the Creator and created reason.
The Pope explains that Christian theology and the Greek philosophies of reason did approach each other once and this is also a challenge for us today.
Then the Pope explains three phases of de-Hellenisation within Christianity. First the Reformation which strived to simplify Christian theology and cut it from its philosophical roots, then the Enlightenment, where faith and reason were put into two different compartments and then modern liberal theology which reduces itself to the simple message, denying the philosophical and mystical parts of belief in the Divinity of Christ and the Trinity.
Behind this third phase stands the modern form of seeing reason purely in a materialistic way, the matter in a mathematical structure.
The Pope argues that western society has put reason into a purely positivistic frame work which excludes other wider forms of reason.
And this, he argues might be dangerous even lead to pathologies, which necessarily break out, when reason is shortened in such a way, that it excludes the questions of religion and ethics. Ethical rules reasoned through evolution, psychology and sociology are just not sufficient.
And the Pope concludes that reason which is deaf to the Divine and thrusts religion into the area of subcultures is unable to a real dialogue of cultures.
The whole lecture was highly philosophical and read in context there is no way that it could have been intended in any way as a provocation towards the Muslim world.
The question is why the New York Times together with other media outlets which have done its own important share in the "clash of civilization" rhetoric chooses now to paint the Pope into a new Crusader?
Could it be that in publicizing the incidence in such a way they just want to stoke up the fires of intolerance and show the Muslim world that the Catholic Church has taken sides against Islam?
For one thing is absolutely sure: from the time of the first Gulf War the Vatican has strongly opposed wars in the Middle East and else where.
With the Vatican envoy in Palestine the Catholic Church has joined other Christian churches in calling Christian Zionism a heresy. Since Christian Zionist churches are the strongest non-Jewish support groups for Israel this comes rather close to denouncing Zionism itself.
It also seems as if the Vatican has been an outspoken critic of Israeli aggression against Lebanon and Gaza recently, although many people think he should do more.
While the Pope is definitely interested in a religious and cultural dialogue, in the building of bridges towards and a peaceful coexistence with Islam, there are powerful forces who are totally opposed to this.
I hope and pray that we Christians and Muslims together with wise clerics and theologians will not fall into the trap of hatred leading to violence and war, a trap which has been set by people who have neither faith nor even secular humanistic ethics.