The recommendation for 200 to 800 IU daily is for people who already have normal vitamin D levels. To correct vitamin D
deficiency, modern sources recommend
a minimum of 1,500 to 2,000 IU daily [1]. The Endocrine Society even recommends 6,000 IU daily [2], so 5,000 IU is not crazy by any means. There is also nothing crazy about five years of supplementation: Many people won't maintain normal vitamin D levels even after five years of 2,000+ IU (unless they make lifestyle changes like being deliberate about spending more time in the sunlight) and they may need to continue vitamin D repletion indefinitely [2, 3].
5,000 IU is probably a bit much to give without rechecking the vitamin D level at least once a year or so, but at least to me it's not obviously medical malpractice. If there is medical error here, it's ignoring calcium levels higher than 11 mg/dl for months and the fact that the patient had to refer herself to an endocrinologist because her PCP did nothing about it.
Overall, I really don't like this article. The author is generalizing based on outlier cases. She even admits this: "Of course, there is a selection bias in who comes to me. There are people out there doing just fine on 5000 units of Vitamin D daily. I only see the ones who develop high calcium levels." She uses "hormone" as a sort of scare word, kind of how "chemical" is used in other contexts. Sure, there are some hormones that can be very harmful, but there is nothing inherently wrong about taking hormone supplements, even for an extended period of time, just like there is nothing inherently wrong about consuming "chemicals."
I strongly disagree about restricting over the counter vitamin D. Tylenol and ibuprofen lead to thousands of hospital admissions and hundreds of deaths per year, and yet we freely give them over the counter. If vitamin D doesn't meet the threshold for OTC, then basically nothing does.
Parts 1 and 3 of the series are better. I agree that the evidence on vitamin D for most things other bone growth in children and osteoporosis is weak.
[1] https://www.ccjm.org/content/89/3/154 ("Increasing and maintaining the 25(OH)D level consistently above 30 ng/mL may require at least 1,500–2,000 IU/day")
[2] https://academic.oup.com/jcem/article/96/7/1911/2833671 ("We suggest that all adults who are vitamin D deficient be treated with 50,000 IU of vitamin D2 or vitamin D3 once a week for 8 wk or its equivalent of 6000 IU of vitamin D2 or vitamin D3 daily to achieve a blood level of 25(OH)D above 30 ng/ml, followed by maintenance therapy of 1500–2000 IU/d")
[3] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2912737/ ("Regardless of initial vitamin D therapy, and assuming no change in lifestyle or diet, a maintenance/prevention daily dose of 800 to 2000 IU or more will be needed to avoid recurrent deficiency")