Um did you all play the same Bounty Hunter storyline I did (and I am talking about the actual BH story, not the side quests)? I very rarely KILLED any of my targets, I captured them and returned them to the client. If they kill them afterward, well, it's out of my hands. Seriously... the only people I killed was random stuff you got to kill cause it's an MMO. Actual story people, I killed...
I followed The Bounty Hunter's Creed
which is canon from the comics and games, and by about level 35 had 10,000 affection with Mako, having not given her a single gift. My final alignment at 50 after completing all main and side quests was Light II.
Now, as for the side quests, I realize some of them, especially Taris and Belsavis, can be a bit much, but really the Bounty Hunter doesn't care about light or dark. They aren't force users, so the dark side isn't going to corrupt them. Strong emotions won't make them fall to the dark side, Jedi, Sith, it's all nonsense to them. What matters is the job. Now, the level of that, well, that depends on your character. For a TRUE Star Wars Bounty Hunter, you would follow the Creed. If you think Boba Fett is the "true" bounty hunter though, well Boba Fett WAS IMO a psychopathic killer who used bounty hunting as a way to get legal permission to kill people... there's a reason Darth Vader had to say "NO DISINTEGRATIONS!" to him. Disintigrators are a nasty and sadistic weapon banned in both the Republic and Imperial space. Not even the Imperial Navy uses them!