This is very much an intentional choice by the writer.
Obviously. But if the OP is looking for spotless virtuous christianity, he's gonna be massively disappointed. More often than not the game makes you want to punch your local catholic real hard
You're supposed to be actually role-playing as a Christian in the 1400s, and that means that you can't just chop off the head of the first crooked friar you meet even if you think he's dodgy.
It's about what people in that part of Europe believed at that time.
Tell that to hussites, man.