This is a very difficult topic, one that would involve a very long and very detailed answer. Books have been written on this. they're just making general statements without really giving any physical evidence.
I think, however, that it needs to be realized that there are very different different philosophical viewpoints here. According to modern times, "freethought" is, pretty much dogmatically, the highest good that can be attained. The world can be interpreted in any way that one wishes, essentially, is what this boils down to. If this is accepted, then one must essentially admit that universals don't exist.
Universal truths are "oppressive." They restrict freethinking. You believe what you want, I believe what I want, regardless of what the truth is.
That's what the modernists believe (correct me if I'm wrong). The Catholic Church, on the other hand, holds the philosophy of universal truths that are always truths no matter what people think. In and of itself, this is good, not evil.
Now, naturally there will always be those that refuse to accept these truths, and for the sake of the whole, the church has often times found it necessary (under circuмstances where other options have been exhausted) to burn heretics, excommunicate, etc, in order to preserve the integrity of the whole church and to purge it of sheep in wolve's clothing.
True, there have been very corrupt bishops and priests, but that's to be expected in any organization as massive and widespread as the catholic church. The Church, in and of itself, can never be blamed as evil, as it has a monopoly on truth and is not deprived of anything whatsoever.