Academia then comes back and says that it is exactly this kind of totalitarian thinking that contributed to the evils of anti-Semitism, racism, sexism, and a host of other isms, and that free inquiry allows us to start afresh with the question of how to build a good society.  In short, questions about the Humanities and about religion in particular start to look a lot like political questions, with each side trying to gain an upper hand.  And students are likely to be swayed by whichever opinions they encounter in the classroom, because at least in the classroom they are forced to think deeply about these questions, to move beyond the he-said-she-said rhetoric abroad in many popular media.

Is there a middle ground?  Yes, and it is precisely that middle ground that was the object of study of the Catholic monastic communities that invented universities in the first place.  For Catholic theology holds that the world is knowable because God created it, and that every area of study is worth pursuing because ultimately it leads us to a fuller embrace of the truth of the world -- even when it challenges our current orthodoxies, religious or political or scientific.  Academic freedom arose as a way of insuring that scholars can be free to challenge these orthodoxies -- scholars like the 13th century professor Thomas Aquinas, the Dominican who, following his teacher Albert the Great, imported the pagan Aristotle to discern the nature of human behavior in the world; or scholars like the 20th century professor John Courtney Murray, the Jesuit who (among other things) served on a presidential commission amidst the Vietnam War and argued for the necessity of conscientious objection to some wars. 

Questions of theology and morality are, in their long view, like other questions, in that they ought to be studied and debated in the hope of coming to a fuller appreciation of what's true.  They ought not be zero-sum power games; they demand cooperation, intellectual, and academic freedom, and also responsibility to acknowledge error when it is demonstrated.  They must be beholden only to the fullness of truth, not the needs of the market.

College may indeed kill faith if faith is regarded as private, if questions of faith are regarded as unimportant, or if religion is regarded as a pernicious power game.  Students may learn a trade but they will not learn how to live.  On the other hand, college can nurture faith if it is a place where students' faith questions are honored, if resources from the long historical conversation about faith are entertained, and if those who intelligently practice faith are welcomed as mentors.

Catholic colleges and universities today are, I think, on the whole better than many non-religiously-affiliated schools that are paranoid about offering classes about religion for fear of political dispute.  Catholic institutions -- at least those that are not RGCs -- can draw from about 800 years of academic protocols that are frankly a lot sounder than the politically charged, attenuated versions that abound in many institutions today.