Once again, I bring up nuking nanites out of existance with magic. A nanite-targeting ram/wreck/demolish spell or maybe a nanite-targeting, physical equivalent of spirit zapper.
Also, what happens when a nano-intolerant individual catches CFD?
Rule 1 of magic is that you can only hit what you can see. This is especially true with direct combat spells. The reason it is so hard to target nanites with spells is that even outside of the body, they're too small to see, and inside a body, there's a whole bunch of flesh and bone hiding them.
As for a nano-intolerant individual, the nanites would break down quicker, but since CFD nanites can replicate themselves as long as the person eats, that isn't an issue. May slow the process, but otherwise not going to do anything.
I agree with Firebug that technomancers may be the key to stopping CFD, if only because they can go places and look for code where noone else can. There are many secrets in the Resonance Realms, and only technomancers can go there. It wouldn't be surprising, then, if the answer to Sybil's identity, or especially the key pieces of code that might spell the end of CFD if written into an anti-virus software, were in the Realms somewhere.
Another possibility (which would account for why CFD is seemingly unstoppable) is that Sybil (the original one) is an e-ghost of a technomancer caught in NeoNET's experiments during the whole Emergence drekstorm, and somehow retained her abilities after 'transcending'.

*shudder* Damnit, I'd almost forgotten about those bastards! Make the Borg look cuddly in comparison.
Much as Influenza's stronger strains which screwed up people like Woodrow Wilson and led to one of medical science's mysteries in what's come to be known as the Sleeping Sickness because their brains were so badly damaged by influenza that they couldn't hold onto consciousness.
Besides the technomancer angle already brought up, there's the EMP/HERF angle that was brought up that could be a way of slowing things down - though I think that would only be a very short term solution as both are mentioned to be able to mess up cyberware which is hooked into the body's metabolism for at least part of its energy and integration which is the same as so-far-described nanoware. Sybil has to be at least partially if not wholly dependent on 'hard' manufactured nanites.
Sleeping sickness and the like are exactly what I'm thinking of. A better example may be some forms of cancer, however, especially in this case. You can try cleaning them out as much as you like, using whatever methods you can, but the damage done to that point (both by the disease and your 'cure') still remains, and you can never really get ALL the cancer.
As for EMP/HERF guns, that would only work on hard nanites. CFD nanites build hard and soft nanites from what the infected person intakes. Just from eating, the victim provides the nanites materials to make more soft nanites. If they eat sand or something (which they've been observed to do) they make more hard nanites.
Perhaps if you took scans of dragon (or more likely shifter) neural pathways you could upload that to the victims and give the virus fits. Of course while this was in place those cured couldn't use the matrix without risking going insane but if the alternative is being erased?
Well, dragons definitely wouldn't cooperate and a lot of shifter difference could be due to innate physiological differences that might be impossible to duplicate even with nanites (and using those leads us back into the problem again).
You're both assuming that dragons and shifters can't be infected with CFD. While I suspect it would take much longer than in others, there is nothing in the information we have that says non-metahumans can't be infected with CFD. Yes, that includes nonsapient critters, such as devil rats or the common housecat. The only reason it hasn't made the jump from metahumans to others is that apparently CFD victims can control how 'infectious' they are. At this point, I think we should assume that the only ones not susceptible to CFD are nonphysical entities, such as spirits, sprites, and AIs.