The author argues against using a particular equation when certain conditions required for that equation do not hold. He further points out that "the most interesting plasma physics occurs precisely where and because this equation is not satisfied, such as the auroral acceleration region, magnetic field reconnection, turbulence, shocks, and many wave modes."
Read that sentence carefully. He's saying one cannot use a particular equation to describe magnetic reconnection. But do you know what that means? It means that the author is saying that magnetic reconnection is real. He's saying that if one isn't careful, one can handle it incorrectly, but he's also saying it's a real and interesting phenomenon. Furthermore, he is NOT claiming that everyone who works on magnetic reconnection is doing it wrong. No such claim exists within that paper.