We can't observe anything "directly", other than the contents of our own minds. The "gravitational discrepancies" are an observation.
It seems to me (non-physicist, non-cosmologist) that DM proponents can't tell us what DM is, despite being able to observe it. The article's "nightmare" is that it might turn out to be impossible to do that in principle. To my mind, that would indeed be a nightmare; we would have to accept that there are limits to what we can learn about the Universe. I don't believe we have encountered any such limits before.