I consider the difference between reality and the way the game works just creative license. There's a lot of stuff that just wouldn't work if the game tried to adhere to some kind of realistic parallel. That said, the game favors evil in most respects. I always take the evil choice in ethical decisions. When it comes time to choose an alignment, the fee for Neutral is pretty minor really. The fee to select "good" can be substantial, but I haven't played good alignment since Dread Lords.
I think it would be better if the alignments were more balanced, as noted above, a choice between bonuses. Neutral isn't terribly far from evil in that respect, but Good always gets the short straw. I have not yet found a compelling reason to play it again.