The former. The author has been posting about this since 2009. From the comments section of TFA:

> I trust people who 1) respect basic principles of science … such as “don’t just ignore dozens of well-done studies that run counter to your hypothesis”, 2) don’t require donations from Big Food and Big Pharma to exist, and 3) take our evolutionary history into account when deciding which foods are likely good or bad for us. The AHA fails on all three counts. - Tom Naughton

Probably some combination of the two. The "science" around diet and exercise is thoroughly corrupted by huge amounts of money from various companies and people that try to push the results in directions to benefit themselves.

Even the valid and reproducible studies out there seem to be twisted into into overly hyperbolic claims by companies looking for profit or bloggers/journalists looking for views.

I think it is more like the innovator's dilemma, as applied to a non-profit organization. I wouldn't go so far as to call them "morally compromised".

It kinda sounds like they're a non-profit public health organization that profits by harming the public's health. Am I missing something?