First things first, you have to remember that you will not auto-target bounty hunters in a fight, so if you are beating up some liberty rouges and bounties come along, there is a chance you will end up killing them too.

Always verify your target, and once bounty hunters are the only ships left, run like mad. Never fire back at them, even dying is preferable to killing one. Also watch that you haven't pissed off any shipping companies, because bounties will automatically attack you no matter what if you get near a shipping company that hates you.

This obviously can then lead to accidentally killing some of them.

Another thing: Don't shoot those storage containers under Storage Depots, the massive tanks on some of the space stations, freighters, transports or anything else that looks like it might be carrying a lot of cargo... Even if the bounties dont see you doing it, they will still hate you for it...

However, bounty hunters are turn-coat scum and are despised by all of the criminal world (moreso cos bounties are ex-crims and therefore know many base and jump hole locations). Personally I'd just shoot them. They are nothing but pest, and every criminal organisation will love you for killing them. Police & Navy factions wont even care either, so feel free to hunt the hunters near planets and everything!