I’m going to give you an argument describing why i think you’re correct but also why you’re getting pushback. I’m basing this off the greek discursive appeal structures i’ve been reading about lately, because its fun to try to apply them here.

Firstly, if people say its a great ‘scientific study’ where you hear it, correct them. Its sad but thats often all we can reasonably do. If they refer to it as a great study in humanity, then maybe it is. After all Supersize Me was about the mostly unconsidered and wildly successful upselling technique that had passed into the culture of the time. So, what does that say about us?

Pathos

Supersize Me is an exercise mostly based on an appeal to Pathos. An argument based around an emotional appeal.

My stab at the key emotional switch employed would be turning the blasé attitude around the then common, comfortable upselling practice “would you like that supersized?”, to a feeling of angst when those words are spoken. I think Supersize Me was largely successful in that appeal.

Emotional switch: Blasé->Angst.

I found Michael Moore’s documentary styles also relied heavily on Pathos. So maybe the style was de rigeur at the time.

The big question is, did these documentary makers pass from persuasion into manipulation? This is the same as the question your asking when refering to his undisclosed alcoholism during filming. Which is why i think you’re argument that the documentary wasn’t fairly done is right. Theres a manipulation at its heart.

But that doesn’t defeat the very real effects that emotional switch from blasé->angst about the practice had.

So a successful but manipulative documentary?

Logos

The argument i read in your comments assumes the documentary should primarily appeal to logos. Or a persuasion tactic based in logic. No controlled experiments for example.

While there are probably plenty of examples of this throughout the documentary, I wouldn’t say this is the primary appeal he relies on.

The obvious conclusions of the poor diet is a good example of an appeal to logos. But not very persuasive on its own, because no one needed to watch it to draw the conclusion that poor diets equal poor health. At least most didn’t.

Another thought,

Its a documentary, its not necessarily an exercise in absolute honesty. Few documentaries can claim such an authoritative place.

I think its maybe why Louis Theroux has belatedly become so highly respected. Not because he was authoritative in the beginning, but so much of what he presented has since been borne out. Maybe his documentary series matched the changing realisations of the times, so have had a kind of Kairos?