If something feels morally wrong for a person for a certain issue, I usually respect those feelings. Unless their opinion and the actions that come from it could somehow end up harming other people.

As for religion affecting moral beliefs, I think it's okay because if that's what they truly believe and they are okay with believing it then others should respect that. Unless it affects others in a negative way (sacrificing other people to their gods, restricting what people can wear, etc.) But if those people that are being affected are okay with it then it's okay.