Basically, the article can be summed up as both incendiary and shocking; I can see why Gene Steinberg attacked it.
If Budd Hopkins were to tell his side of the story, my hunch is that he will have nothing to defend himself with. Ms. Rainey argues that Hopkins worked with little oversight, no protocols to automatically fact-check, and he universally rejected (or ignored) critical input from other researchers. So there is nothing that he will be able to pull or furnish, either from the case files or from verifications presented at the time, to support his research, other than his unswerving belief that he was correct.
I thought that the article was an interesting refresher and backstory to cases that I followed, with varying degrees of interest, at the time. I bought "Witnessed" when it was first published; and I remember that the case was soundly attacked, not by debunkers, but by other paranormal investigators. One researcher "outed" Linda Cortille by publishing her real name, much to Hopkins' anger. The book was published when the Internet was still nascent, so it wasn't possible to fact-check the book, but I spent some time trying to identify some of the pseudonymned key characters. After a year or so, I forgot about the case.
I remember the Jim Mortellaro story very vividly, because the case was given wide exposure on the paranormal radio shows. If I'm not mistaken, he appeared on the Jeff Rense show, and I remember that he gave the most harrowing and detailed abduction encounter story that I've ever heard, before or since. He struck me as being completely authentic and truthful. That Ms. Rainey is able to easily and effectively discredit his story is significant: because while most of "us" can spot the phonies very easily, Mr. Mortellaro seemed to be real deal (to me, anyway). Was this because he had the sociopath's gift of being utterly convincing while recounting untruths, or was it simply that I had stopped applying the most basic level of filters or skepticism to abduction accounts? (I say it's the latter.)
Most UFO or abduction researchers that I've heard often defend their research by using the circular argument of, "I know that this case is true because the witness sounds absolutely credible to me." In fact, I would wager that some of the most significant cases in UFO literature depend solely on how truthful the witness seemed to appear, with no supporting documentation. The Mortellaro case shows the significant danger of such an approach.