How about making a new arch-nemesis, but not naming him Blofeld? That would suit both the reboot-feel and the awesome sense of continuity. So, quintessentially, the head of the Quantum organization is Blofeld, but without the name or the looks. Or, you know, the cat.
I feel that's the way that EON were going with Mr. White. It would have been a great twist to find out that Bond had captured Quantum's head, only for him to escape. The opera scene in QOS only added fuel to the fire for me.
I always saw Mr. White as more of a middle-man when it came to Quantum , rather than anything close to the head of the organization: In Casino Royale he is the one that sets up the deal between the Le Chiffre and Obanno and takes care of Le Chiffre when that deal goes wrong, if Mr. White was the head of Qunatum having him personally kill Le Chiffre would be slightly odd as he could send anyone else after him.
He also had something to do with Vesper (most likely the contact she gives information to before it is sold off) which would be a surprisingly lax approach to security for the head of an Organization, because if Vesper ever decided to repent they would be able to track him down with relative ease (as we see Bond do) and in the Opera scene he does not actively take part in the discussion about Bolivia...Greene is very clearly in control of this meeting (presumably if White was the head of the organization Greene would ask his permission or defer to his advice in much the same way Largo and Blofeld interacted.)
If anything I think we can assume that Greene and White operate on similar levels (but their is another man above them all) from memory the description we got of the deleted scene with Guy Haines at the end of Quantum was that Mr. White was shot and killed by Bond in this sequence while in a meeting with Guy Haines, which could even suggest that Guy Haines outranked him in Quantum.