Honestly, I never thought Dark represented evil. They kinda repeatedly mention that Pokemon aren't inherently good or evil, it's their trainers that make those moral choices. In my opinion, Dark just represents trickery, deceit, and "dirty" tricks. Take a look at the Dark type attacks; Faint Attack is a deceptive attack, Biting is considered a dirty way to fight, Thief steals items, etc.
The reason Fighting is super effective against Dark is because Fighting type represents more "honorable" fighting, like the martial arts. The idea is that dirty tricks and deceit are no match for disciplined combat.
Dark is super effective and immune to Psychic because their deceptive nature prevents Psychics from reading them correctly.
What I don't quite understand is Dark's weakness to Bug and effectiveness against Ghost. shrugs No theory is perfect I guess. :)