The vitamin D theory still may fit in with a virus theory. Rummaging around the internet I found a few studies stating that Vitamin D is an antiviral. So it's not out of the realm of possibilities that a low Vitamin D level, combined with a virus, and maybe even other factors, could produce a perfect storm leading to what we call MS and/or CCSVI.
Of course these are wild speculations on my part (merely for the sake of discussion though), but the MS story seems to be much more complex than just a simple virus or vitamin deficiency alone. For example, EBV is found in something like 95% of the population. Vitamin D deficiency is also prevalent in our population, especially in North America/Europe. These may all be necessary factors, but the evidence does not suggest they are sufficient ones.
Low vitamin d levels in the womb could program the genes to be predisposed to certain vascular malformations or just veins that are unable to fight off viruses. Then, when a virus in fact invades the body the vessels could collapse, become malfunctioning, etc.
I think the evidence is out there, we just need more processing power to put it all together. Then again, I'm no scientist, just thinking outloud.