They're somewhat always inherently "extremely mildly pathogenic" (I guess "asymptomatically parasitic" describes better) in the sense that they're always piggybacking on the host's resources to replicate. Whatever is the level of non-pathogenicty, it generally doesn't imply a commensal relationship (if there are viruses thought to be commensal, that's new to me, I'd be interested in reading more on it), it's more like just being "sneaky," having only a level of activity that doesn't trigger a significant immune response - which ironically is often part of the pathogenesis itself, it can be more so than what the viruses are doing directly, which perhaps may be one sneaky way of wording a wider "non-pathogenicity" of viruses. Not saying that it's what happens in the article, which I didn't read.
But they're AFAIK always parasitic, even if non-pathogenous in some cases. Whether they can be "desirable parasites," well, that's more of a weird philosophical question than a scientific one, given that most people, non-masochists, wouldn't desire being targets of parasites, regardless of how "sneaky" they are in stealing resources.
What can be said that would approach some kind of "desirability" would be in some way that they "help evolution," but then it's not different with virulent pathogens and even mass-extinction-level meteor impacts, except that those are more noticeably harmful. It's more of a nonsensical point of view that adopts entropy as a "goal" for the universe or something, rather than real-world human experiences. Although there may be some way to phrase this ecological role without seeing evolution as a "goal" and their eventual role in things like horizontal gene transfer or natural selection as "helping" it in a human-level way of "help." More like lions are "helping nature" in killing zebras or people and so forth, meaning doing what they do, part of a network of somewhat balanced interactions, but with no magical "greater good" in some way analog to creationism.