The content of the article is specifically using the alleged unfair dismissal of Loeb's ideas to argue the broader point that the scientific community unfairly dismisses unconventional ideas in general. I agree with you that the counterargument above is not validly refuting the article as a whole, but it is definitely making a non-fallacious refutation of that specific sub-argument.

Put another way: the sense of the counterargument is not that this opinion piece itself is a fringe/crackpot idea, which is what you'd expect if the counterargument was simply "This is from a crackpot." In fact, it's not dismissing the content of the article at all. The counterargument is admitting the logical coherence of this opinion piece - that if, among other things, Prof. Loeb's works are unfairly dismissed, then it demonstrates a closed-mindedness in the scientific community - and attacking the premise by saying that the works in question were in fact fairly dismissed.