There's nothing wrong with serious endurance exercise or sport. The problem with the guy in the article that you linked to, "Case Against Cardio", is that he was doing it the stupid way, the way most people are told not to do it. I have never hear of his so-called "popular wisdom of the past 40 years – that we would all be better off doing 45 minutes to an hour a day of intense aerobic activity" and to "aerobicize at the chronic and sustained high intensities".
Now after 40 years he has realised that he was doing it wrong. Good for him, but he must have had his head in the sand for 40 years and trained in a very closed group that did not learn anything in those 40 years.
Did someone really tell him to do it that way? I have never heard that or read that in the last 40 years.
Anyway, for weight loss, I believe that, like most things, different things work for different people. Walking does nothing for me for weight loss, even if I walk 10-12 miles daily I stay the same weight. However, I know someone who lost a lot of weight from doing the exact same thing. For me, running 40-50 miles a week does help me lose weight but running 20-25 miles a week is not enough for me to lose weight.