I don't believe the pontiff knows everything, though. He was already shown not to even know why Potimas is collecting kids, even though he was smart enough to realise there must be something significant behind it. I also feel like trying to murder masses of fellow humans because of a simple doctrine difference is exceedingly stupid. Even though in RL it's a problem in the Middle East now and was a problem in Europe some hundreds of years ago. However, unlike us, the pontiff lives in a world with horrible monsters led by a demon lord and also non-human humanoids, who aren't necessarily friendly, like the elves. Kind of strange to have massacring other humans as his first priority.
I do admit your other points about Potimas are quite solid. He has some flaws that make it hard to believe he's only interested in saving the world, for example, instead of saving the world by making others than his own people pay the price. It's still a bit weird the teacher has been so willingly going along with it. Do you think she's evil as well?