By being the sole center of learning and scholarship in the European Dark Ages, by giving birth to the modern university, and by inventing musical notation?

Yes, I am aware of the bad things too. Reality has nuance.

Edit: Now that I think about it, you are certainly right that the Catholic church has done more gross harm than Scientology, if only because it is much bigger and has been around for more than twenty times as long. However, I am not sure how the net harm stacks up, due to its central role in the founding of Western civilization, and other mitigating facts.

I think "learning and scholarship" is stretching the truth - the primary caretaker in preserving ancient scholarship, yes. But what new research and learning was going on? The really hot stuff was going on in the Arabic world at that time. While the monks were carfully copying old books, Al-Khwārizmī was busy moving forward.