The problem is indeed there, but if the goal is to find out the human coherent extrapolated volition, then a definition of human is necessary.
If we have no way of picking out human minds from the space of all possible minds, then we don't really know what we're optimizing for. We can't rule out the possibility that a human mind will come into existence that will not be (perfectly) happy with the way things turn out.* This may well be an inherent problem in CEV. If FAI will prevent such humans from coming into existence, then it has in effect enforced its own definition of a human on humanity.
But let's try to salvage it. What if you were to use existing humans as a training set for an AI to determine what a human is and is not (assuming you can indeed carve reality/mind-space at the joints, which I am unsure about). Then you can use this definition to pick out the possible human minds from mind-space and calculate their coherent extrapolated volition.
This would be resistant to identity-space stuffing like what you describe, but not resistant to systematic wiping out of certain genes/portions of identity-space before CEV-application.
But the wiping out of genes and introduction of new ones is the very definition of evolution. We then would need to differentiate between intentional wiping out of genes by certain humans from natural wiping out of genes by reality/evolution, a rabbit-hole I can't see the way out of, possibly a category error. If we can't do that, we have to accept the gene-pool at the time of CEV-activation as the verdict of evolution about what a human is, which leaves a window open to gaming by genocide.
Perhaps taking as a starting poing the time of introduction of the idea of CEV as a means of preventing the possibility of manipulation would work, or perhaps trying to infer if there was any intentional gaming of CEV would also work. Actually this would deal with both genocide and stuffing without any additional steps. But this is assuming rewinding time and global knowledge of all human thoughts and memories as capabilities. Great fun :)
*coming to think of it, what guarantees that the result of CEV will not be something that some of us simply do not want? If such clusters exist, will the FAI create separate worlds for each one?
EDIT: Do you think there would be a noticeable difference between 1900AD!CEV and 2000AD!CEV?
It’s the year 2045, and Dr. Evil and the Singularity Institute have been in a long and grueling race to be the first to achieve machine intelligence, thereby controlling the course of the Singularity and the fate of the universe. Unfortunately for Dr. Evil, SIAI is ahead in the game. Its Friendly AI is undergoing final testing, and Coherent Extrapolated Volition is scheduled to begin in a week. Dr. Evil learns of this news, but there’s not much he can do, or so it seems. He has succeeded in developing brain scanning and emulation technology, but the emulation speed is still way too slow to be competitive.
There is no way to catch up with SIAI's superior technology in time, but Dr. Evil suddenly realizes that maybe he doesn’t have to. CEV is supposed to give equal weighting to all of humanity, and surely uploads count as human. If he had enough storage space, he could simply upload himself, and then make a trillion copies of the upload. The rest of humanity would end up with less than 1% weight in CEV. Not perfect, but he could live with that. Unfortunately he only has enough storage for a few hundred uploads. What to do…
Ah ha, compression! A trillion identical copies of an object would compress down to be only a little bit larger than one copy. But would CEV count compressed identical copies to be separate individuals? Maybe, maybe not. To be sure, Dr. Evil gives each copy a unique experience before adding it to the giant compressed archive. Since they still share almost all of the same information, a trillion copies, after compression, just manages to fit inside the available space.
Now Dr. Evil sits back and relaxes. Come next week, the Singularity Institute and rest of humanity are in for a rather rude surprise!