I disagree with most of the argument in the article, and it seems pretty heavily fueled by some anti-Nike feelings.
You're basing this whole thing on "unfair additional assistance" provided by the shoe, stating that it falls outside the purpose of the shoe as defined by the IAAF as "to give protection and stability to the feet and a firm grip on the ground." Then you go on to state a bunch of studies that show 4% improvement to running economy and the time that would save an elite marathoner. That's all great.
So why should the Vaporfly's be banned according to the article? Why do they work so well? Because "with their huge stack height, they effectively extend the length of the leg, and, with their foam and carbon plate(s), help a runner store and return energy." So by this logic any shoe with any stack height in the heel would be extending the length of the leg and should be illegal? And any shoe with a sole that can help a runner store and return energy should be illegal? Because these are things that every shoe does. I suppose technically, under the IAAF rules, it might fall under giving "stability to the feet," but this whole Vaporfly argument is under the pretense that its the only shoe providing any benefit in any way. Every single shoe helps a runner store and return energy. Compare barefoot running with running in any shoe. Shoes give improved running economy. They either all break the IAAF rule or they don't.
Where does that leave the argument? You could still say that Vaporfly's provide "unfair additional assistance," but it all boils down to how unfair is defined. Does Letsrun.com get to define it, or maybe Nike? It's silly to argue whether or not the shoe gives an advantage. Nike clearly has the best shoe available right now and every other shoe company is playing catch-up trying to make a similar model. But you're taking about nullifying Olympic results because Nike has a superior shoe and all other companies have inferior products? Every shoe gives energy return and stack height, Nike just made the one that does it best. That's not unfair. This is a ridiculous argument.