The article is very perceptive and accurate.
The first mistake was forming a commission. The second was allowing the commission to come to a consensus, have that consensus signed off on by nine cardinals and archbishops, then wait TWO YEARS before responding with an encyclical that reversed the commission.
Once the commission's opinion hit the press, the argument was over. Humanae Vitae was, by the time it came out, an afterthought.
Once the pope assented to the regulation of births, the method became incidental.