Not only did the Pope say—in a thinly veiled attack on extremist Islam's justification for terrorism—the concept of Holy War goes against nature of God, he also blamed West and its secular rationalism for excluding God and alienating other cultures. This, notwithstanding the fact that Christianity, thanks to the encounter between the Biblical message and Greek thought, welcomes intellectual inquiry and always reveres the truth.
This leads directly to the issue of “faith and reason,” which is apparently the most important of all in the papal address.
The encounter between the Biblical message and Greek thought did not happen by chance. The vision of Saint Paul, who saw the roads to Asia barred and in a dream saw a Macedonian man plead with him: "Come over to Macedonia and help us!" (cf. Acts 16:6-10) – this vision can be interpreted as a "distillation" of the intrinsic necessity of a rapprochement between Biblical faith and Greek inquiry.
In point of fact, this rapprochement had been going on for some time. The mysterious name of God, revealed from the burning bush, a name which separates this God from all other divinities with their many names and declares simply that he is, is already presents a challenge to the notion of myth, to which Socrates’ attempt to vanquish and transcend myth stands in close analogy. Within the Old Testament, the process which started at the burning bush came to new maturity at the time of the Exile, when the God of Israel, an Israel now deprived of its land and worship, was proclaimed as the God of heaven and earth and described in a simple formula which echoes the words uttered at the burning bush: "I am". This new understanding of God is accompanied by a kind of enlightenment, which finds stark expression in the mockery of gods who are merely the work of human hands (cf. Ps 115). Thus, despite the bitter conflict with those Hellenistic rulers who sought to accommodate it forcibly to the customs and idolatrous cult of the Greeks, biblical faith, in the Hellenistic period, encountered the best of Greek thought at a deep level, resulting in a mutual enrichment evident especially in the later wisdom literature. Today we know that the Greek translation of the Old Testament produced at Alexandria - the Septuagint - is more than a simple (and in that sense perhaps less than satisfactory) translation of the Hebrew text: it is an independent textual witness and a distinct and important step in the history of revelation, one which brought about this encounter in a way that was decisive for the birth and spread of Christianity. A profound encounter of faith and reason is taking place here, an encounter between genuine enlightenment and religion. From the very heart of Christian faith and, at the same time, the heart of Greek thought now joined to faith, Manuel II was able to say: Not to act "with 'logos'" is contrary to God’s nature.
Read here the complete text of the lecture, but bear in mind that this text must be considered provisional, since the Holy Father intends to supply a subsequent version of it, complete with footnotes. Read also an anthology by Italian Vaticanist Sandro Magister of the homilies and speeches delivered by Benedict XVI during his six-day trip to his Bavarian homeland.