According to the NWN Wiki:
Fear is indeed a mind-affecting effect. So it should get the PfA CoA bonus, since the CoA bonus replaces the immunity that is normally given.
The Fear Spell however only has the Fear descriptor, not the mind-affecting descriptor. This is silly in my opinion, since fear is classified as a mind-affecting thing, so protection from alignment should apply to the fear spell. And if it doesn't, we should change it so it does.