It sounds a bit mad until you think about it. Their faction isn't the one that issued the bounty and so they don't care about the bounty at all. They just view it as a plain old murder.
Think of it like you are out on the town with a few friends and one of them gets arrested for something you do not believe is a crime. Are you going to agree with the arrest if you don't believe your friend is guilty? This is the same thing but with guns
Ever notice that the Federation sends out pirate killing missions in independent systems?
Ever notice those pirates are part of the leading factions in said system?
Or perhaps the missions involving killing traders?
The USS's with a lone pilot begging you to stop killing innocents and cancel your pirate mission?
I am starting to notice that the Federation is a bit ruthless with its agenda. It may offer some Independent states their freedom by it's own accord, such as Van Maanen's Star, but others they have been using mercenaries to destabilize their government and annex them when the federal party gains power.
I had a hard time bounty hunting two days ago when I kept getting fined. Mind you I attacked Clean pilots that had bounties in the contact window. This did not work well at all.
...12k bounties against me for every kill of a local party with minor bounties on him.
I started making money legitimately when I started killing Wanted vessels labeled as wanted on the front screen. The bounties where being paid by the local system I was in rather than federation. However the targets seemed to be giving me bad rep with federation upon destruction, otherwise they where part of the local mob.
You cant help or hurt anybody without one party benefiting and another taking the short end of the stick; likewise, they pay their reputation with you the same.