Sure, CPUs do all sorts of things better than GPUs. CPUs are great at managing interrupts from multiple devices like USB, PCI, etc. CPUs are great at managing memory spaces, protecting system resources from other threads of execution. And so on. None of those have anything to do with hashing algorithms that make the blockchain secure.
We add things like interrupt management and memory protection to CPUs because of the way people typically use CPUs. What's fundamental to a CPU is the ability to accelerate random accesses to memory, to make program flow decisions, and so on.
The beauty of the Bitcoin hashing system is the asymetric nature combined with robust security. Incredible amount of computing power to find a hash, but trivial to verify the hash. I suspect that this new SC "design" is going to mess it up.
Typically the hash verification takes place on a CPU anyway. In any event, you could make hash verification take several hundred times more computing power and memory than it requires currently and it would, for practical purposes, make no difference. The only thing you'd need to change is, perhaps, DoS protection against nodes that stream blocks with invalid hashes at you.