B16 is apparently wrong about the age of the Surah in question, the Western philosophical tradition is not short of proponents of absolute omnipotence (Descartes,) or deniers of various foundational bits of Aristotelian logic (such as Aristotle himself), and sometimes both together (d’Autrecourt),
1. The Palaiologos passage has clearly been taken out of context; B16 did say that Manuel was brusque, and it should be obvious that the emperor wasn't in an ideal position for rational debate.
2. There is such a thing as freedom of speech after all; B16 was well within his rights to make the case against the narrow concept of reason now regnant.
3. That Catholics haven't always lived up to their obligations to reason in the past doesn't disqualify them from making their case now.
4. Anyway, B16 has, nobly, twice apologised, each time specifically disavowing what'll no doubt come to be known as the Palaiologos position.
B16's just not the bad guy here.
Tariq Ramadan has a response to B16 here, and again, here.