First off, I never said the church WAS evil, I said it has done many evil actions. And that's the same in the manga- We're just focused on the corrupted elements of the Manga Church because they're the ones starting racist holy wars. In the same chapter we meet Ether who is a very nice individual church member, and we learn that there are multiple nations within the Yeesus faith with doctrinal and political differences. Some are less evil than others.
I can't agree that it's useful to separate political entities with the institution, I think they are diametrically tied. The institution (Culture, doctrines) are derived from the material entities (people, places, external culture influencing, etc.) that adhere to it. And through history the "beliefs" of the church have been adapted to match the culture around them. For example consider how different catholicism is in America than in South Korea or in Brazil.
To your point about libraries being culpable for the crimes of the military, I don't see how that absolves the military (which acts with institutional authority). If you mean to say that institutions don't do crimes, smaller groups of members do crimes; yes, obviously. Institutions are metaphysical concepts made up of groups of members. Like I said, they are diametrically tied. Institution as superstructure, Members as infrastructure. Another important point is when members do crimes and the institution leadership doesn't condemn them.
I see your point about making value judgments about what is evil or not, so I'll start with some broad institutional accusations.
One, that by the 4th century the Church was a landed interest with a ruling class. Certainly there are fringe cases of benevolent ruling classes, but I'd say in general you don't become rulers by playing nice. Anyways you find plenty of examples of the ruling authority abusing their power.
Corruption, bribery, selling fake relics, sexual hedonism, indulgences, living in largesse at the expense of the people, excommunication of political rivals, covering up widespread sexual abuse, and
waging intersectarian war. As stated before, these are both the crimes of individuals, yet widespread and protected by institutional leaders.
Two, that Christianity uses in group/out group identity to justify violence. Often to attain power/wealth for the ruling class. That includes violence against non-Christians, and sectarian violence between Christians. Starting with
Paul of Tarsus advocacy of missionary work, it has led to centuries of "Christian MIssionaries" justifying
exploitation and genocide. (This one in particular is the example in the manga. Fake Catholica is waging a colonial war using religious justification). This includes Christian missionaries in Feudal Japan who sought to incite armed insurrection and conquer the island for Christianity. It's no wonder that Japanese culture finds the Church shifty.