My 2 cents is that you don't have to take the PrC to play an assassin. Don't attach too much to what the class actually is, just what it represents mechanically. Play a rogue.Does the assassin class HAVE to be the stereotypical hired contract killer with no morals or scruples? (is that even a word?)
Or is there room to play an assassin who is "just following orders" and better at sneaking around the dark than running all over a battlefield in platemail armor and towershield.
In the same way, while there is a paladin class to represent the "knight in shining armor", a LG fighter or cleric could represent the same, depending on how it's played.
Just because the "Assassin" PrC is not on your character sheet doesn't mean your character can't be an assassin, in the same way that not all characters with "Rogue" on the character sheet are burglars and thieves. RP should determine what's on your character sheet, not the other way round.
Finally, in DnD, good and evil are black and white. It's a failing of the system. Most "evil" characters think they're doing good, anyway, or are somehow justified. The typical insane and misguided villain who thinks he's doing everyone a favor by destroying this cold, barren world where nobody's happy doesn't classify as chaotic good, he's chaotic evil.
In the same way, "misguided good" in the DnD system can quite easily be labeled as simply evil. Isn't that what evil is, after all? Good gone bad?