I HATE Farnese
Sometimes i think Miura has a sever distaste for any christian themes (can't blame him) and goes out of his way to utterly destroy/disprove any relevant bearings it would have on the story. Ie. Farnese going from zealous witch-hunter to magical apprentice.. it doesn't fly with me. Seeing her burn that poor baby bird was the last straw.
Well, keep in mind, the young Farnese is basically unhinged from straight-up rich-kid neglect. You're not supposed to like her, exactly, but you're supposed to recognise that she is, like everyone in the world of Berserk, largely a product of her circumstances. And, I assume, you're supposed to empathise with the way she wants to change when her world expands beyond what she has known up till then.
She was a witch hunter because she was a tiny, lost thing, and taking control of the fire was the only relief she knew how to get. The catalyst for her change was seeing how wrong she was about having any control in the first place. Her pursuit of magic is her choice to face the problem of being a small thing in an ancient world, and to learn how to relate to it instead of railing against it.
The popular religion in Berserk is very intentionally not Christianity, or even Catholicism, in the same way that the Midlands are not Germany and Vrittanis is not in Italy. Miura uses a lot of the real world as source material for building the world of Berserk, but I wouldn't mistake it for a straight allegory or anything. It's borrowing a lot from Catholicism of course, but to whatever extent the events of Berserk are actually meant to be allegory, they are allegory for fanaticism, for mob psychology, for what people do when confronted with extreme adversity. In short, for organised, hierarchical religion as it relates to frightened masses, in general.
And don't forget that we still know very little about the popular religion in Berserk; we have no idea whether it's associated with a real god or not at this point, or if it's strictly man-made, or if it's an intentionally hollow religion crafted by darker forces with the express purpose of misleading the masses. All we know is that it's been easily co-opted by the powers Femto has on his side.
We only know that previous religions were definitely associated with real entities, because Schierke knows how to contact such things. And even Schierke softens her initial scorn in Enoch when the preist agrees to honor the older spirits there.
We don't even actually know who sent the vision, or what effect it will eventually have on the story. At the moment it's helping Griffith, and we assume it was sent by the God Hand for that purpose, but it's at least conceivable that at some point people might see things that change their mind about what it meant.