Going back to the holding up a store at gun point... If the shop keeper refuses to pay, and you shoot him, is that not changing the crime from armed robbery up to murder?
So in short, I don't see the difference. If you as a Pirate interdict a non-wanted CMDR and open fire and ultimately murder/destroy them... Hard cheese! You've made a dangerous move! As a Pirate you should instead be intimidating them into paying up, or at worse damaging their ship to such an extent it makes sense for them to pay up, or such that you can forcibly take the cargo. Piracy should not be about permitting murder!
That said, that's why I think the game needs to open up plenty of "legal" avenues to murder/destroy CMDRs! Indeed, I'm sure pirates could be give missions to periodically murder CMDRs to distrupt/destabalise systems. ie: The missions would be to kill a member of the Pilots Federation in system X or Y within Z days... The mission giver would *hand wavium* hack/cover up the murder so it would not count against the player... This would actually give the game a control over "random murder" too in keeping with other underlying mechanics! eg: If a system needs destabalising for a reason, offer more such murder related missions.
Couple of potential issues with this...
If you are a pirate, and murder is so much more punished than assault, then the 'victim' has more cards to play than you do, knowing that the likelihood of the pirate using such force would end up potentially ruining their game (in the end, these punishments need to be game breaking if they are going to do anything to stamp out the anti social behavior that these ideas are proposing to address). It's really just the opposite side of the coin we have now, that there are no real consequences to murder. Likening crime in the game to crime in RL isn't really a good indication of how things might work out IMHO.
As to legal avenues for murder, yes, I think these should exist (PvE too), hence my previous posts regarding the crime punishment system. But... To have the possibility for legal / sanctioned PvP murder, then FD open up a huge can of worms for any CMDR who might not have explicitly consented to PvP, and that stands to make the current discussions seem very tame. "FD sanctioned another player killing me without my knowledge and consent?" I can see how that might go down...

Obviously just my opinion.
I remember in previous Elite games, deep space was largely open for any action, and that was fine since there could be no 'exploiting' of the mechanism by players, and you could happily take a murder contract to kill a governor or senator, and as long as you didn't do it outside of a station, you didn't become wanted. If FD went down the road of creating real anarchy systems, and there was a very clear indication that a player was entering one and would therefore be fair game, then perhaps some of these ideas might work. Might...
I would add that at that point, they really would need to consider an official PvE Open mode for players who want the social side of their MMO without the aggressive side.