I think Ockham is the primordial source of the problem. More specifically, it is Ockham's notion of freedom that is the source of the problem. Ockham's radical voluntarism is the historical root of the notion of autonomy. Ockham's nominalism is the origin of the attack on metaphysics (especially natural theology). Now, Ockham further replaced natural law theory in ethics (and consequently the Patristic/Thomistic view of salvation as deification) with a divine command theory in ethics. Now, when we join a divine command ethical theory with a vountarism like Ockham's, the result is a huge shift in perception of what it is to be human and what it is for a human to stand before God. I admit, the resulting picture is psychologically intolerable, and so Ockhamism engendered a reaction to Ockham's image of God and Ockham's image of the moral life. That reaction takes the form of, first, Protestantism and, second, atheism.
To see the implications of Ockhamism spelled out in detail, I highly recommend a book by the Belgian Dominican Fr. Servais Pinckaers. Title: "The Sources of Christian Ethics". Catholic University of America Press, 1995. (For those who might be intimidated by the large, scholarly work of Pinckaers, there is an abridged version called "Morality: The Catholic View" available through St. Augustine's Press.)
Pinckaers, I think, was a ghost writer for "Veritatis Splendor", and I am convinced that he wrote the sections of the Catechism on the Beatitudes and the New Law. Once you read him, you will see what I mean.
An essentially Ockhamist view of freedom is what lay behind Kant, Nietzsche, Sartre, the whole gang.
John Paul II knows this perfectly well, and so has made this very theme, that freedom is essentially ordered to truth, a key theme in virtually all of his writings. JPII is striving to overturn the Ockhamist notion of freedom and replace it with St. Thomas' intellectualism.
This is why I am convinced that of all the Popes since Trent, JPII has the deepest critique of modernity. Prior Popes have attacked modernity, but only at the surface level where it was least vulnerable. JPII has gone to the root. The difference between (JPII and St. Thomas')notion of freedom and our own (Ockhamist) notion is so radical that it takes years to purge oneself, and one's interpretation of the Catholic faith, of Ockham's corruption.
Tridentine Catholicism, implemented mainly by the Jesuits, was itself insufficiently purified of Ockhamism. And this insufficient purification eventually caught up with the Jebs. They are now essentially Protestants, and on their way to atheism. This is not to say, of course, that Tridentine Catholicism contained error. It is merely to say that Tridentine Catholicism was band-aid solution to a deep, deep problem that is the root of Protestantism and Secularism. Vat II removed the band aid, and now we have one bloody mess on our hands until the wound of a thousand years is really and truly healed.
Richard Weaver said the same thing in 1948 with his timeless conservative classic, "Ideas Have Consequences."