The Pope is exhorting the academic world to accept that theology has something very important to say to the "scientific ethos" if it is "to be obedient to the truth".
"... In this sense theology rightly belongs in the university and within the wide-ranging dialogue of sciences, not merely as a historical discipline and one of the human sciences, but precisely as theology, as inquiry into the rationality of faith.
"Only thus do we become capable of that genuine dialogue of cultures and religions so urgently needed today. In the Western world it is widely held that only positivistic reason and the forms of philosophy based on it are universally valid. Yet the world's profoundly religious cultures see this exclusion of the divine from the universality of reason as an attack on their most profound convictions. A reason which is deaf to the divine and which relegates religion into the realm of subcultures is incapable of entering into the dialogue of cultures."
He intended "dialogue of cultures" to refer as much to the dialogue between academia and theology as it does to social cultures, it appears.
The reference the Pope made "...of Christianity and Islam, and the truth of both..." and much later the inclusiveness of his statement "...the world's profoundly religious cultures..." makes it clear that he supported Islam's inclusion in this exhortation that theology be considered part of the academic culture when he said, "A reason which is deaf to the divine and which relegates religion into the realm of subcultures is incapable of entering into the dialogue of cultures."
His thoughts about Islam itself may be given on another day, but it was not that day.
"The reference the Pope made "...of Christianity and Islam, and the truth of both..." and much later the inclusiveness of his statement "...the world's profoundly religious cultures..." makes it clear that he supported Islam's inclusion in this exhortation that theology be considered part of the academic culture"
No way. This is your misreading of the opening discussion of the differences between Christianity and Islam and equating them with zealous Christian belief. The Pope is clearly negatively referencing and tying the concept of Jihad to Islam's discard of the logos that is central to Christianity.
I read in an allusion to those anti-religious (fundamentalist atheists) who disparage all religious belief by pointing to the excesses of Islam. To them the Pope says, no, we are not like them. Our beliefs are grounded in logic and tempered by reason.