Even though these characters are not the traditional Blaster/Scattergun-Stealthy-Scrappers Scoundrels, they are described in universe as being Scoundrels
You obviously missed the point I made, and that's because I have typed it out so much on these forums over the years I didn't really want to do it again. I wish I could have provided the link to the Developing the Bounty Hunter blog, but it's no longer in the list of developer blogs on the site. So now I'll explain in greater detail...
Each player of a class, for the purposes of Star Wars lore, is playing the exact same character
as every other class. No matter how many warriors there are, they all are the same warrior who becomes Baras's apprentice. No matter how many knights there are, they all become Orgus's apprentice.
Are there smugglers working for the Empire? Yes. But the character the players are playing is the very best smuggler in the galaxy, which happens to be aligned with the Republic. The very best trooper in the galaxy is aligned with the Republic. The very best bounty hunter and the very best agent in the galaxy are both allied with the Empire.
Sure, the Developers could have made a story for a Republic aligned Bounty Hunter, and thought about doing so. Would a Republic Bounty Hunter be cool? Sure, but in the films both Jango and Bobba Fett fought against the Jedi. And in order to implement a Republic Bounty Hunter, they wouldn't have had the room to make the Republic Trooper.