His point was that the best defense against the spreading of faith through force is to point our the irrationality of it. His complaint is not so much against Muslims for being Muslim. It is against western scholars for excluding religion from their scholarship. That the wall that we have erected between faith and reason has done a great disservice to both sides. That the marriage of faith and reason that we see in Hellenized Christianity allows us to insist on a rational God and allows science to understand where it fits into the bigger picture. Here is a quote:
This gives rise to two principles which are crucial for the issue we have raised. First, only the kind of certainty resulting from the interplay of mathematical and empirical elements can be considered scientific. Anything that would claim to be science must be measured against this criterion. Hence the human sciences, such as history, psychology, sociology and philosophy, attempt to conform themselves to this canon of scientificity. A second point, which is important for our reflections, is that by its very nature this method excludes the question of God, making it appear an unscientific or pre-scientific question. Consequently, we are faced with a reduction of the radius of science and reason, one which needs to be questioned.So what he is saying is not so much that Islam is bad. It is. What he is saying is that Western Christianity is headed in the same direction as Islam. That the marriage between faith and reason is breaking down and we will get an irrational religion and science disconnected from meaning and purpose. If you see theology as the queen of the sciences then the whole world is open to the rational mind. If you make logic and empirical observation the queen of the sciences then you either have to make the humanities fit or exclude them from scholarship. You end up not only losing theology but losing the hard sciences as well.
I will return to this problem later. In the meantime, it must be observed that from this standpoint any attempt to maintain theology's claim to be "scientific" would end up reducing Christianity to a mere fragment of its former self. But we must say more: if science as a whole is this and this alone, then it is man himself who ends up being reduced, for the specifically human questions about our origin and destiny, the questions raised by religion and ethics, then have no place within the purview of collective reason as defined by "science", so understood, and must thus be relegated to the realm of the subjective. The subject then decides, on the basis of his experiences, what he considers tenable in matters of religion, and the subjective "conscience" becomes the sole arbiter of what is ethical. In this way, though, ethics and religion lose their power to create a community and become a completely personal matter. This is a dangerous state of affairs for humanity, as we see from the disturbing pathologies of religion and reason which necessarily erupt when reason is so reduced that questions of religion and ethics no longer concern it. Attempts to construct an ethic from the rules of evolution or from psychology and sociology, end up being simply inadequate.
There is a reason why christian scientists are so devoted to their pursuit of the truth. Even if they are not very good Christians they often have enough of the christian world and life view that they believe in an ordered creation. They believe in the inherent good of learning about that order. It is really a desire for God even though many would not use that word.