The whole interview is worth reading, but I liked the following analogy.
How important is academic freedom in the vision of John Paul the Great Catholic University?
I like the analogy of a baseball field. In a baseball field, when you’re out in outfield, there are wide open spaces, you can hit the ball wherever you want. But when you’re inside — home plate or wherever — there’s a dugout and stands with definite boundaries. Faculty cannot take positions that are at odds with the teachings of the Church. On the other hand, the Church allows great freedom in terms of how you can implement the teachings of Christ. There are huge opportunities in all the "dos" of the teachings of Christ and the Church. There is enormous freedom… that’s the outfield. There are a million things people can go do which are not inconsistent with the teachings of the Church. Just play on that part of the field. Academic freedom at our university means you need to follow the rules and then, within that framework, take advantage of all the freedoms you have.