That's the problem with a lot of domains... there's nothing inherent in a lot of them to denote any sort of morality. Some domains do denote morality-- protection is generally "good", murder generally "evil"... but things like Civilization, Nature, The Seas, Determination, Magic etc.-- they can be used for good or evil. And thus there's no reason why the deity for it should have a set alignment in my opinion. Or at the very least if the pantheon is going to be anthropormorphized a la the Greek pantheon for example... the personalities of the gods should not get in the way of the reasons for their worship, nor should the worshippers all default to the god's personalities too. Just because a god of the sea is listed as "evil", it shouldn't follow that all worshippers/clerics/priests should be evil too. That just seems pointess.