Commentary:

Virology has only weakly scientific methods

The strongest evidence in favor of viruses (IMO) is experiments involving filtration, as with tobacco mosaic "virus" or rabies

Hypothesis:

There are potentially pathogenic microorganisms much smaller than ordinary bacteria, but they are spore/seeds/larva (etc) of ordinary microorganisms, not obligate intracellular parasites

Analogy:

You rip up a forest, pass it through a filter too small for trees to pass, plant the remaining material, and in a few years you have trees. Thus you conclude the trees are just a "response" of the soil to some other forest-causing agent. Obviously we can realize that seeds/nuts/fruit are much smaller than trees but grow into trees. What if eukaryotes/bacteria/fungi (etc) have such mechanisms as well?