I will disagree with the professor because there is no struggle between science and the supernatural. The simple fact is that science cannot deal with the supernatural since by definition the supernatural is things outside of nature for which we have no empirical evidence. Science only deals in things we have empirical evidence for or things for which we think empirical evidence can be found.
So there is no struggle against the supernatural, science does not compel scientists to materialism simply because the the material world is the only thing we can study empirically. You can't say that we are forced to material explanations since there are no other explanations that provide us with empirical evidence. I note that no example is given of case where a "non- material" explanation is in any way useful or explanatory let alone more useful or explanatory than a empirical materialist answer.
It is not that science cannot allow a divine foot in the door, it is that we require a divine footprint we can measure, and as ever anything supernatural evades any hint of measurability.
The counter-intuitiveness of the material world (I would also argue that is an indication of our own lack of understanding rather than anything 'wrong' with science) is irrelevant to the question of any supposed conflict between science and the supernatural.