Guide Ahead's antagonist Andoain is broken by hearing his state's refusal to support the Iberian faithful in their dire straits; the need for help is irrelevant because of the victim's ethnicities. The crisis of faith is an awakening for him, a moment of realization rather than just despair and creation of a villain. GA-8:

Mostima falls saving Lemuen from Andoain, a pure act of defense and is punished for it. When Andoain fires on the Pope and is fired back upon, neither fall. It wouldn't be hard to interpret that as Law, religion, being judicial, protecting those in power and giving them special treatment rather than helping or understanding a situation like Mostima's. GA-7:

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Hortus De Escapismo features a town struggling to survive, Sankta and Sarkaz working together to resolve low food and supplies. I believe this is more about understanding than necessarily religion, but even it is not subtle. As soon as Laterano becomes involved, the situation quickly deteriorates and very nearly becomes a bloodbath. All of the people here could be assisted, fed and cared for, but dogma states that some simply do not deserve. That even if some disagree, they will still accept that broken stance. HE-5:

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The Masses' Travels opens with a look back in time where it is proven praying has no apparent physical effect. The focus is instead emphasized that it is about wishing others well, having them in your mind. A divinity is more a circumstance to invite this expression of empathy, not the reason for it. MT-ST-1:

MT-10:

However, instead of understanding this lesson it ends with the country and religion utterly failing to empathize, nearly resulting in atrocity. You are not a part of us and do not deserve respect, so we will make you part of us and you will earn respect. MT-7:

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Break the Ice has my most hated character in the game, the Vine Bead Court Elder, poisoning others for their political opinions, ones that would weaken the Court's power. Instead of descalation or mediating the situation between the three major clans, as is their purpose and authority, they tamper and make it spiral further. BI-6:

They regularly detest the Silverash clan for the progress and innovation they bring to Kjerag, but undoubtedly also due to the risk this presents to their stranglehold on the country. God I hate the Great Elder.

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Retracing Our Steps 1101 is all about the Vine Bead Court feeding Kjerag to Victoria in a bid for power, led by a man who explicitly did not believe or have faith. He repeatedly built up a lie, killed and deceived to maintain it, rather than help those around him, rather than have faith that they would remain steadfast. OS-ST-3:

OS-10:

Would-be saintesses are forced into a one way climb, freezing to death one after another chasing for a concept even as they would have been able to help their families. The Goddess herself is even horrified by this. OS-10:

Pramanix's punishment for the clerics led astray was to live and participate in the work of the common man. To assist them while considering how to better apply Kjeragandr's tenants. Not to reaffirm their faith, but to better understand it so that they may better help one another. OS-ST-4:

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The seaborn saga is less focused upon itself religion as a core element, but even the Cult of the Deep and the Seaborn in general demonstrate its problems. Their bishops summon the apocalypse and turn people into fish, but they do this because they know what's best for you; so join, assimilate, abandon your individuality, and survive in this lessened state. Masses' Travels is practically identical in its messaging.

In Exodus Across the Pale Sea Anastasio is crazy and kills people who would readily join the town, destroying resources and lives for their supposed 'sin.' A vague, irrelevant notion, while Silver tries his best to actually help the ailing town. As this excellent post makes clear, despite Anastasio being the more 'devout' and 'righteous,' he completely lacks actual, meaningful faith.

Raisengen's post about the Yurodstvo highlights it as a weaponized personification of all of these vile effects of organized religion.

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To me, these points are hammered home again and again that faith and belief belong to your family, friends and neighbors. Microcosms and examples of these themes are everywhere.

Degenbrecher and Gnosis repeated trust Enciodes, following his plans and barely scraping by each time. With how little explanation he gives it starts practically becoming faith. Gnosis fumbles Monch because he didn't believe in or trust her.

The Londinium saga has a huge element devoted to the civilians rising up and saving themselves rather than waiting for a greater power; represented with the absent dukes all busy vying for their own ambitions. The Exemplars storm and retake Londinium themselves.

The greatest tragedy of the game fits exactly into this archetype! Oracle believes more in the grand plan of Originium, and betrays Theresa! They could have had faith in her, likely won the Kazdel civil war, but chose a far away notion ordained by Priestess. Priestess, of course, being a character referred to as the Creator, Theresa as Prometheus who stole fire from God.

I would argue even on a meta level nearly every single level you play in the game is operators choosing to trust the Doctor with their positions and tactics. Even if you're bad at the game, you can trust a stronger unit to carry you through, or trust another person's guide.