The seemingly perennial debates surrounding Catholic universities in actualizing their claimed Catholic identity seems to revolve around the concept of "academic freedom." To be frank, higher education in general succeeds and is a benefit to society when all questions can be asked and people are free to inquire and research.
The problem is that academic freedom, as it is currently preached, is not truly practiced. Most universities, in general, hold to a secular humanist ideal where the mere mention of religion is restricted. Entire departments and fields on inquiry are restricted to one particular position. Try to get tenure in cellular biology and dissent from the embryo-destroying stem cell research dogma. Try to defend the traditional family and get hired into a sociology department. Good luck.
For decades, left-wing professors and administrators have silenced debate on their closely held doctrines. As a result, they simply don't have any way to defend them because they don't have to. Question affirmative action on campus and they cudgel you with racism charges. Speak out against gay marriage and you're an intolerant homophobe. In some places, donating to a Republican campaign is a career-ending decision.
There would be nothing wrong with liberal professors or liberal institutions on campus… if they were actually open to debate. With panel discussions being mostly political rallies, something has got to give. In the context of Catholic universities, there are plenty of critics of the Catholic Church in higher education. Most places simply don't allow any defense of the Catholic Church.
The higher education system works largely because of they great diversity of universities in the system. There are plenty of colleges to choose from if you want to be thoroughly immersed in the secular humanist ideal. Why is the system under such great danger if a Catholic institution wants to be actually Catholic?
If a university is honest about its perspective and disposition with new students and new faculty, there is nothing wrong is being true to its claimed identity. Professors who wish to thoroughly investigate why the Catholic teaching on abortion is wrong will find a home at a near infinite number of religious studies departments across the country. Yet, when a Catholic college wants its faculty to be actually Catholic (or at a minimum take Church teaching seriously) then they are waging a war against academic freedom. Whatever happened to academic honesty? If you don't really believe it, don't teach in an environment that claims to.
These fights have started and grown in intensity because the university system has largely banned conservative lines of questioning. Far from trying to take over the university systems to indoctrinate, it's time to really have the free exchange of ideas. If this can't take place in the context of a campus, at least allow universities to exist that allow for those lines of questions.
No ideology grows and thrives when it seeks to eliminate any and all criticisms of it.