So instead of them being straight villains, they're the ignition point for a medical revolution within the human kingdom.
The problem is that MC is doing the same thing with more technical knowledge, less politics, and a LOT less racism.
Yea, but both things I like.
There's villains in the church - but they ain't all villains as is the more common manga trope. (Just like there's been the occasional "good pope" even in our world)
And even the godly plan is pretty smart, since the medical revolution is still something that will work a lot better alongside the magical treatments - but it can work without the magic if needed, so the human skills remain valuable but their total monopoly on quality healing breaks.