If something were to be done like that then a CQ wipe would definetly be the way to go.
As for the way I think the points should work, i'd say base it off of a PvP MMO I played before this.
Someone suggested using the chevron ranking system for players also, so when thats meshed with the RF system it would work something like:
• A rank 1 kills a rank 2, he would gain 2CQ the rank 2 would lose 3CQ.
• A rank 1 lands the final blow on a rank 3, same as above except +3/-5CQ is exchanged.
• A rank 1 gets instapopped by a rank 3, no CQ gain/loss would occur.
• A rank 1 gets killed by a rank 2, the rank 2 gains 1CQ, but the rank 1 loses nothing.
• A rank 2 gets killed by a rank 3, the rank 2 loses 1CQ, the rank 3 gains 1.
• Killing someone of the same rank would grant you the same number of CQ as your rank (+/- 3 at rank 3 for example)
• Someone in a group lands the final blow, that person gets max CQ, while the rest of the group recieves 1.
• This ones not really needed...but, if someone kills a player more than 25 Levels below them, they lose 10 points. (50's would avoid killing people under level 25, but the -25's would be able to poke at them for 1 damage =p)
NOTE: The RFO system worked in a much different way i'm just thinking how it could be applied here. For example there, if i had 100k CP (Contribution Points, basically CQ) and I killed someone with 10k CP i'd gain practically nothing and they'd lose nothing. If i killed someone with 300k CP, I'd gain about 4k and they'd lose around 10k. Basically the bigger the difference the more it affected your CP change. But that game was literally made for ONLY pvp (perma-flagged from level 1) so the system probably wouldnt work well here.
So what this system does is:
• It rewards lower levels to be somewhat feared in PvP as they would suck alot of CQ if they landed the final blow somehow. (I remember the lowbie killing rampage I went on in RFO after a lowbie Summoner landed the final blow on me and sucked away 9k Contribution Points >.>

• Prevents cheating by letting someone kill you repeatedly to get thier CQ up as you would lose CQ in the process.
• Lets lower levels *try* to help in PvP without much fear as they dont lose any CQ from anything other than rank 1's. (Getting to rank 2 is where you start to lose CQ basically)
• Gives much needed fear of dying in PvP. (Other than ego reasons)
• Will most likely cause more red names as everyone would want access to the rewards mentioned below.
• Forces the "I have to oneshot this lowbie to try to *CENSORED* him off" type of player to have a bit of honor....or just kill the lowbie anyway and lose the CQ
And now..the negatives:
• Might cause people on the non-pvp servers to flag less frequently. Might need to go the SWG route, where if you get flagged somehow, you'd be flagged for the next 30-45mins even if you die.
• Will give the higher CQ players a much larger e-peen >.>
• The amount of 'I just got ganked' threads on the Vector forums would crash the forums.
• The amount of work needed to implement even half of this will probably cause it to never happen.
And now, we all know that there has to be a reason for having high rank/points in any pvp system.
So what I was thinking is, having vendors that require X amount of CQ to access.
For example, a vendor that sells misc. fun items like fireworks and whatnot could be available at 500CQ, while a vendor that sells highly coveted pvp gear could be accessed at 10 or 20k CQ. Of course this doesn't have to be limited to vendors, new areas can be accessed at X amount of CQ (that have mobs that drop good loot for example), let players convert CQ into info (at the cost of losing the CQ they transfer to info), new abilities that can be purchased with CQ (imagine purchasing a new finisher for your fighting style =o), the sky is the limit.
Of course this wouldn't be able to be put into effect until all classes are balanced and whatnot (read: when 95% of players arent SMG Specs, MKT's and Kung-Fu, afterall..how many Proxy Masters or Vectors do you see running around. Bet you didn't even know there was a class called Vector =p). But even in the classes current state, I think having a point to PvP would be pretty nice.
And as a final thought, with all the talk about WoW, it made me think of battlegrounds (for those that don't know, they're basically instanced pvp arenas). Imagine how cool it'd be to team up with fellow machinists hop into an instance where you have to prevent the mervs from achieving X objective. I might as well stop now...going off on a limb, guess its just too late and my brain is fizzling out. >.>
/endrambling