Having played the Smuggler storyline (darkside) I'm going to say there is no reason that I wouldn't work for the empire if they offered the creds. I'm a sick little twist, killing and betraying people left and right usually in the name of money. I'm not a "bounty hunter' of course, as I'm generally not hired to kill people, but to move objects and information, which is surely a service the Empire could use as well.
Personally I think IA should have been the mirror for troopers and BH/Smuggler should have been mirrors. They should have had their own spiffy planet to start in and, at level 10, you choose your faction. I suppose for ease you could still keep the BH 'title' as Imp and the smuggler 'title' as Repub (IE you pick your faction and become Bounty Hunter Whatshisface) And form there you would go about whatever storylines were crafted.
Ah well, whatever. I maintain that I'm not loyal to the republic, and took the option to rob them at the end of my storyline. Glory to my bank account!