The title of the article is an intentional conflation of "systems thinking" with "magical thinking", which is not a compliment.
I think there's plenty to agree with in the article's descriptions of failure and hubris. What the critical commenters are taking issue with is that the article blames those symptoms on a straw man. It's a persuasive article, not a historical review, so it's reasonable to debate its conclusion and reasoning as well as its supporting evidence.