This is an interesting idea, thanks for sharing this article.
I do think he's on to something. I've seen some of this evidence before and while it's a bit preliminary, I think vitamin D supplementation could carry risks if you have impaired conversion of the supplementary form to the active form of vitamin D.
This conversion ability probably varies depending on the person, but one of the main factors affecting this is magnesium deficiency, which runs rampant in countries like the U.S.
This may be yet another example of the fact that no nutrient works in a vacuum. There are frequently risks incurred from massive supplementation of otherwise highly beneficial nutrients without regard for the other nutrients which play an important role in its regulation. For example, Chris Materjohn has written a lot about the interplay between vitamins A, D, and K(2) and how they help mitigate the toxicity of each other.
We're dealing with a lot of speculation, but I'm hedging my bet on even fairly large doses of vitamin D posing very little danger to a person replete in vitamin A, vitamin K(2), and magnesium. This is obviously a niche highly unlikely to be represented in your average vitamin D supplement study drawing from the population at large, but more likely among the paleo and WAPF eaters.
And I still think there's lots of research supporting vitamin D levels as a casual factor in reducing disease risk, although the idea that D might be low as a consequence rather than a cause of disease is an interesting one that may be true in some cases.