I always had a bone to pick with Arknights' portrayal of the Inquisition and its cruel policies as actually necessary, down to the Evil Cultists actually having infiltrated the country through the exchange with Aegir and the Inquisition actually having found a good portion of the people they took from Gran Faro to be working for it (including Thiago's lover).
But thinking back to it more deeply that's pretty much in line with Arknights' usual approach; the game has a fairly consistent habit of presenting the most idealistic versions of various ideologies in order to still strike them down as wrong despite that: Vina's father really was a stereotypical "Good King" who wanted to help the people yet still couldn't accomplish anything under a feudalistic system, which led to the literal King Arthur stand-in refusing the throne because she thought the monarchy should end with her; the Witch King really was a genius individual better than anyone else to a supernatural degree and that still didn't stop his downfall and descent into madness and he couldn't protect anything more than a false image of Leithanien perfectly curated for him because any system entirely depending on a single individual is going to fall and there's no merit in an ideology that doesn't allow for weakness and leaves everyone else behind; Aegir really is a more advanced civilization who maybe could actually improve the living conditions for all of Terra but that doesn't stop the story from being very critical of their hubris and their attempt to forcibly impose their will on the other nations; Columbia really is often motivated by scientific passion and is making serious progress at incredible speed and that still doesn't stop its capitalistic and imperialist ambitions from getting in that way of that passion; and so on, there's plenty of examples.
The Iberian events consistently show the Inqusition as unjust and cruel, at times focusing on the aftereffects and the suffering brought by their rule even more than the suffering brought by the Seaborn. Does it really matter if their strict and authoritarian measures were necessary to keep Iberia stable in the wake of the Profound Silence, if the citizens are left so scared of the Inquisition they'd rather join the Church of the Deep anyway? It became an infinite loop where they kept doing everything to violently repress the cultists and that only pushed the people more into despair and straight into the cult that was actually treating them better and giving them food and offering an escape from suffering and hope for the future. The citizens in Exodus from the Pale Sea only survived in their isolation and overcame the scarcity of resources thanks to the Inquisition's rules, but doing that made them so scared, paranoid and devoid of any desire for anything that could make life enjoyable that even after their material situation got better they still didn't dare eat more than the little they had always eaten until now and kept controlling and judging each other for wanting things. It got to the point that when they finally had an actually good Inquisitor trying to make their lives better and to get them to stop following obsolete traditions they didn't understand why he would try so hard to do that and kept clinging to the old ways way after their usefulness ended. And of course Anastasio's entire character is the biggest proof of how warped that entire mentality could be; fanatically following the Inquisition's teachings to the letter made him the the most evil and dangerous Inquisitor we've seen in the game until now by far, while characters like Irene are shown in a far better light explicitly because she's learning to expand her worldview and to seek her own answer and judgmeent rather than solely listening to the scripture.
Arknights' take is basically like... yeah the Inquisition ended up being useful to survive in an extreme apocalyptic scenario where the entire society fell into utter chaos after being attacked by the literal ocean. It still sucked ass so much that people were living better when they were ruled by a warmongering and arrogant king, their entire culture is in shambles and plenty of villages are full of people who act like they already died. For Sal Viento being taken over by a literal horror cult that worships sea monsters improved their living conditions. Even if all the Seaborn disappeared, if this rule continued it'd still be one of the worst places to live in the entire game.
