I think the lesson to be learned from the Shakor incident is that mortal heads of state or similar dignitaries have no place flying around in space in the EVE Universe. For as long as capsuleers have little weapon restrictions and remain virtually immortal, mortals who draw their ire will simply be killed the moment they appear in space. The only way to survive capsuleers as a high-profile mortal is to avoid them altogether.
Currently, I see some people on the forums trying to find acceptable methods (RP, mechanics, and game-balance wise) to have 'essential' NPCs survive when targeted by rich, well-armed, willfull and immortal adversaries. Rather than trying this I would say that the NPC world needs to adapt to the realities posed by the capsuleers class: a clone-less Heth will die if he sticks his head out in space and capsuleers become aware of him. Similarly for a cloneless Jamyl and other high-profile people.
Heads of State aren't (as a rule) stupid. They must be aware of the dangers of capsuleers, and either they would counter them (by disarming capsuleers in high-sec) or they would get clones. No current world leader would live very long if they allowed immortal soldiers with sniper rifles to walk around their countries unimpeded.
Rather than inventing complicated mechanics, I would simply have the NPCs adapt to the day-to-day reality they live in. That would make the most sense.