Very interesting article! Yes, without knowing anything about genes and replication the early virus researchers had no chance to come to a meaningful conclusion.
But still I think that the viruses are protein capsules with genes inside. This concept is - even if not fully proven - the only one that completely explains all observations, and besides we know the sequences of those genes and what they are doing (e.g. some are enzymes that replicate RNA, some are proteins for the capsules, some are responsible for invading the host cells).
However I highly appreciate your skepticism. By the way, there are types of microscopes which can resolve even individual atoms. Or this is maybe all fake? Hard to believe.
In order to "see" something so inconceivably small, I have the imagination that we humans would have to shrink ourselves to the size of an entity that fits on the tip of a pin a million times over. What kind of device can do that? What idea do you have of an atom?
For me, it can only be a linguistic one, a translation of what we are able to understand with our senses. The science which deals with the microscopical realm has developed since the modern age into an abstract science. I experience that it argues reductionistically, speaks in metaphors, because the observable space remains very restricted, if not closed.