In the first Star Wars: The Old Republic developer blog concerning classes, principle lead writer Daniel Erickson explains why Bounty Hunters are born to be bad.
The universe of Bioware's Star Wars: The Old Republic is going to be one of clearly defined good and clearly defined evil. Erickson outlines the goals that the development team laid out in creating the classes of the game - every class has its own story, and no two classes work for both sides of the Jedi versus Sith conflict. Hence, Bounty Hunters are the bad guys.
This was Star Wars™, not Star Neutral Guy's Adventure. When there is a war that spans an entire galaxy, nobody can stand on the sidelines. Sure Han is unaffiliated for about six minutes of the movies, but that doesn't last long, and even if he's not with the good guys he sure doesn't like the Empire. The war affects everyone, even if they'd rather it didn't.
This doesn't necessarily mean that the Bounty Hunter class is evil. It just means that their role fits better in the darker side of things. Let's face it...if you want to hunt other sentient beings, you generally aren't going to be a puppy cuddling kind of guy.
Developer Blog: Creating the Bounty Hunter [Star Wars: The Old Republic]