Well, I don't quite know how it could be made so that you can only claim bounties from people who you are neutral/friendly with. I think that anonymous bounty pots would just be simpler and much easier to create, and make just as much sense in RP.
Though, one thing I do think can be done is that it be made so that you only get the pay-out if the ship you killed was hostile to you (i.e. IFF was red to you), which I'm sure would not be too difficult. I added a little part about that to the main text.
Edit: Well, I'm not entirely sure how it would be possible to restrict the areas where one could get a pay-out from a particular faction (as I'm not a FLHook expert), I'm also not sure quite why one would want to restrict where the hired killer of one's enemies can be paid for doing so.