But then why does slaying them give you negative points? Would not the ones who sided with you be happy to see their politicial rivals sabotaged?
Who cares about your whines? Will you take the case to the court? You've just slain a govt officer on duty. Scapegoating HIM would undermine the whole political structure, and is characteristic for govts which are about to completely disintegrate. In a more or less stable country, you blame the usual suspects instead. Some people might indeed be very happy you did that bastard in, but a govt as a whole coalition of factions - and the international community - is generally a bit upset. You killed a bad general, but we're all bad generals, so... Heck.
What you say would make sense for a targeted and paid for assassination, but such stuff, if you're a legit govt, is better done by own people, not some outsiders.
PS. Unless, of course, say, Eurosyndicate wants to do a Le Suis Govt General. But if it hires some idiots to do said General in, it naturally plans to immediately terminate them after the job. As you can see, for many reasons, gameplay included, your pirate gang is ill-suited for such a scenario.
Also, yes, I plan on adding some 'failed states' missions, where, for varied reasons, you don't get penalized but rewarded for killing govt forces. But this doesn't pertain to general, random cases where you fight a Govt because it just turned out that way.