Right, I've now read through the speech and my understanding of it is that it is a discussion of how faith and reason interact, and what is appropriate for the Christian Faith.
The excerpt from the dialogue between a Muslim and a Christian is used to show that the Christian believes that God can only work in a way in accordance with rationality. The Muslim, by contrast, believes that forcing God to behave only in ways which are in accordance with rationality limits God.
There then follows a long discussion of how Greek (which seems to be used as shorthand for 'rational') thought and Christianity became linked and then three separate periods where some attempt was made to unlink them again - for example because the essential message of Jesus was being burried in theology and philosophy.
If I am reading this thing correctly, the Pope concludes that science is incredibly useful and must not be rejected (he actually includes a dig at the ID loonies) but it is not the be all and end all. He makes the point that if God is reduced to behaving only in accordance with Western rationality, then it denies God's (no doubt to him) obvious part in non-western societies.
In other words - again, if I am interpreting this correctly - he is actually saying the Muslim guy from the short extract all this fuss is about was right to say 'God is not restricted to the rational' and the Christian bloke was wrong.