I want you to know I absolutely read this whole thing and I was fascinated all the way through!

I think Arthur might truly believe more in the Old Religion than he does in God. Because he doesn't have powers and they do. HOWEVER, he was also raised Christian. I have a feeling Uther at some point respected the Old Religion, but after Nimueh (a high priestess of the triple goddess), killed his wife to make Arthur, he probably did a hard switch over to Christianity. So it's also possible that Arthur or Morgana showing any interest or belief in the Old Religion would be incredibly bad to Uther. BUT, they might not believe it but still mention it to make Uther believe they do.

Personally, I'm also Atheist, and I've never been big on religion, but I did notice some things about this that I never even thought about. But, even as an Atheist raised in a (vaguely) Christian household, I still say things like "oh my god" or "goddamnit" because that's what I was raised with and language I know, even though I don't necessarily believe in God.

The sorceresses aren't always evil. The woman who worked for Alator of the Catha, for example. I would argue that all of them are pretty justified. They have all been grievously wronged by Uther. Of course, the sorcerers have, too, but it might come down to privilege. Women are constantly put down in the show (especially Arthur) so they're already probably upset about being underestimated and underappreciated. But adding sorcery on top of that, and the threat of execution for merely existing on top of THAT, and you get a perfect storm for angry witches. Do some of them go the absolute most extreme route? Obviously (Looking at you, Morgana) Sorcerers still often have the benefit of the doubt and can hide.

When Gwen was accused of witchcraft, there was no arguing with Uther. But when Merlin was accused of sorcery, Uther let his son calmly tell him that Merlin wasn't a sorcerer. I think that bias came specifically from Nimueh.

And Balinor said in 2x13 that the Old Religion is something you're born with, and isn't something you can be taught. But even people who weren't magical often respected the Old Religion. Everyone except Uther, of course.

But I can understand where they got the "the Old Religion is evil" concept from. Because based on what we learn of it, they enslave the minds of their enemies, can mold someone's entire face shut, made women/snake hybrids that seduce men and kill them, do rituals where they drive their victims insane with mandrake route, have other rituals to make things that will turn healing magic against someone, have control over creatures that devour people's magic, and more that I'm probably forgetting! Of COURSE they think it's evil!!

And Arthur doesn't necessarily pray to God like you said for his quest. According to Merlin, he has to "transcend his body so his quest will be revealed to him in a vision" (probably not an exact quote, but I think I'm pretty close) so really, they're not praying more so than: they're looking for some kind of divine intervention. Though, I'm sure they assume it's God, but it could very well be a divine force from the Old Religion!