The problem is that there are some characters you can't kill and others you can't spare. And the distinction is arbitrary.
If you can't spare Master Jarro, what reason is there to spare Gault? If you can't kill Gault, why do I have to kill Master Jarro? The reason that a Lightside Bounty Hunter gives to Jarro as to why he needs to kill him is that he has a code that he always keeps his contract. Except there is literally no way that is true because he didn't bring in Gault. A Lightside Hunter's merciful choices essentially amounts to a character that spares and kills people at random.
Second the whole premise of the Bounty Hunter's story is that he's only dependent on money, which frankly feels flimsy. Why do I need the money? I'm not any poorer than any other class of player character. The other three Imperial characters are actually forced to be in the situations they are in and still can somehow get away with disobeying direct orders in some cases. Yet the one class that is ostensibly the one independent Imperial character is actually railroaded the most because they are always participating in a professional murder competition and always for greed and glory.
Sith Warriors can commit outright treason by helping the enemy on occasion. In Act 1 at least, Sith and Agents can be given explicit orders to terminate someone and just ignore it,.
My reply contains some spoilers, so doing the "right" thing and tagging it.