The post is interesting and I haven't read the entire thread yet, but ultimately I'd suggest the proposed methods are a bit too 'in-depth' and complicated for my liking. I'd simplify as follows:
CMDRs who gank another CMDR, should receive noteriety that doesn't go away and bounties on those CMDRs should be unlimited, making them a bigger and bigger target the more they gank.
Once a CMDR ganks someone, their bounty goes up on a new 'PVP Mission Board' (Or gets added to the standard mission board, but is clearly marked as a PVP mission). The payouts need to be high, because the difficulty is very high, but it would provide a rewarding gameplay loop for all concerned. Gankers gonna gank, they're not just bored, they're arseholes and that isn't going to change, so we may as well make a play loop out of it. This way, they get to choose their 'criminal' gameplay path and others who want to 'avenge the fallen' get to kill them and get rewarded heftily. The player has an 'all points bulletin' placed on them by the mission, so their location is constantly updated whenever a CMDR or NPC is in the same space as them, so regardless of where they jump to or hide, other players can find them. The higher the noteriety and bounty, the more NPCs they meet and the closer they are tracked.
This doesn't require an 'opt in' system, or for the mechanics of the existing game to be massively overhauled, the opt-in system is already there with 'report crimes against me'. For BGS and Powerplay, there can be a simple opt in here too, to prevent players getting massive bounties or noteriety when they are actually engaging in powerplay or BGS, rather than just ganking. If the CMDR doing the attacking has signed up to a PVP mission to 'Massacre Squadron Pilots' in the name of BGS, they can do so inside CZ's (Which really should be open only anyway, it's a ridiculous notion that you should be able to drop to Solo and just grind CZ's to undermine a squadron in a MMP game...), because entering the CZ means you've consented to that play type.
Ultimately, to sum up:
1. Gankers (Easily identified by killing a player who has crimes turned on AND is outside a CZ) get persistent (until death) noteriety and ever increasing bounties, all of which is claimable by any player who kills them and both noteriety and bounty in this case, should be attached to the CMDR, not their ship)
2. PVP Missions to kill known 'Gankers' with high mission rewards (Plus the bounty payout) which should always be wing shareable.
3. Open ONLY CZ's where players can engage in PVP as much as they want, provided they have taken a mission and the player they're killing has the affiliated squadron tag (Although, this should probably only happen where it's squadron faction vs squadron faction and not squadron faction vs PVE faction, as gankers would just take a PVE faction mission just to kill CMDRs and annoy people, which defeats the point.)
I think this gives those who want to be outlaws and PVPers the opportunity to still gank, but have to pay the price for it, which is being hunted across the galaxy and the game helping their hunters to find them, while giving those who fancy avenging the fallen a chance to go kill the ganker and it gives squadrons the opportunity to actually duke it out over a system, rather than one or both squadrons fighting NPCs in Solo. All while leaving the existing BGS mechanics in place for wars where there's none, or only one player faction in the war.