I thought that only torturing innocent people or choosing to do evil things (like stealing and fighting guards) lowers your alignment, but does the main quest lowers your alignment from time to time without giving you any choice (or is there any)?

For example I have found my alignment was shifted towards evil after attempting to arrest the paladin deGuise and killing him (I also killed the other paladins that became hostile - this could be the reason?), and after delivering the pagan statuette to that bishop in the garden in exchange for letting me arrest the cult leader.

I'm not sure how it works when you try to arrest Jean de Guise, but as far as that pagan statuette for Severtinus is concerned - yes, this is considered an "evil" quest. And generally speaking - yes, there are some main quests that lower your alignment (like quests involving Tinthan, for example) and there is no way to get around it.