That's the current issue :
Even taking down a Pirate that attacked you first, was Wanted and that you properly Kill-Warrant-Scanned before taking down - it'll give you negative Reputation with whatever Faction he belonged to.
Same with Bounty hunting at NAV Points (do that if you want to lose Reputation with every single Faction in the System, incl. exactly those that issued the very Bounties on those in the 1st place
http://www.falconfly.de/img/chatt.gif )
Same with any Bulletin Mission specifically demanding to take down any Targets (i.e. Pirates).
Everything you shoot will make you lose Reputation.
The only alternative left right now :
- target only Wanted (after KWS) Ships in uninhabited Anarchy Systems naturally belonging to no Faction
- target only Wanted (after KWS) Ships in Independent/Anarchy Systems, about which Factions/Reputation you simply don't care about
The only case I found still seemed to work, was to enter Conflict Zones the classic way, choose a Faction and cash in the Combat Bonds (not tied to any Bulletin Mission). That seemed to leave Reputation alone for once.