I think CCP hinted at making smuggling a player based mission, where the NPCs would go away and only players would stop smugglers. I think that could tie in with your ideas Kaleigh.
As for pirates in high sec, I'm not sure about letting sec status not matter any more to the NPCs and havign PCs take over. But I might suggest the following. Even 1.0 systems have pirate ships in them in the belts, they are just frigates. What about making the NPC only go after people with bad standing if they also have a ship of a certain size. So, frigates can get into 0.9-1.0 systems, destroyers can get into 0.7-0.8 systems, etc. This would fit into the lore and what is already in the game. Then you could add to that your idea on a tiered scale. Say a frigate pilot will never become fair game, but a destroyer would in 0.6 systems and up, etc. Notice I stagered it so that a destroyer pilot will be safe from NPCs in a 0.8 system, but still needs to worry about PCs. Frigate pilots will always be safe in high sec. Or maybe make haulers never fair game in high sec, with frigates taking destroyers place on the list. You could justife it with backstory about bribes and such.
Or, make a new skill, called bribes or something, and make it so that for every level of the skill, you can go into enemy high sec by one level, so at lvl 5, you could go anywhere without beign bothered by anyone. Or maybe it would only apply to NPC, and there would be another skill for PC, but one they could somehow see through it they had another skill. Or maybe just limit it is NPCs only.
Or another idea, this one beint the most technical but in my opinion the coolest. Make a new module like a cloak, but instead of hiding your ship, it disguises it as another ship. Like a cloak, you could not target anyone, and could not fire, but others can target and fire on you. Anyone attacking you will not get CONCORDed if you have a low sec or empire status. But it you are clean, then you are fine and they do get CONCORDed. Now, to use this module, you have to destroy another ship and salvage from it a datacard with that other ships stats on it. Then you plug that into the disguise module like a script and visually, on overview, and to the NPCs you are that other ship, however you still handle like your true ship, so if you are a frigate and you are disguised as a carrier, unless you are careful, somone is going to wonder why a carrier is going 1 KM/s. Also, this module will tell the NPCs that you have the cargo of whatever ship you destroyed, not your true cargo. Player scanners will say the same thing, and will say that you are fitted like the ship you destroyed. You will even have that other pilots info in the show info button. However, anyone who knows that pilot will know that you and not hima nd blow you away. And finally make the datacard expire after a day real time so that the database doesn't get crowded. As another version, you could salvage this from NPCS as well, so that NPCs in missions would not attack you and you could blitz missin by going to the final room and then cutting lose.
So, ideas suggested.