On a molecular level biology is indistinguishable from machinery, it's all just arrangements of atoms doing stuff.
What we call viruses are actually alien nanobots, they're constantly trying to kill us and often succeed but overall life goes on, we're able to live in spite of being under constant attack by these nanobots because for us they're just a feature of our environment. But the aliens that developed these nanobots and deployed them as weapons have absolutely no resistance to them, they never evolved a resistance to nanobots because they don't occur naturally, we only think they're natural because they've been here longer than we have.
These nanobots (what we call viruses) aren't intelligent as such but they're constantly evolving, becoming ever more sophisticated in order to defeat our ever increasingly sophisticated defenses. Indeed some of them don't harm us, they just use us as vectors, some go dormant and wait for our immune systems to be compromised before attacking again, some influence our behaviour (causing coughing and sneezing) to make us better at distributing them.
To the aliens every human is a carrier of an entire ecosystem of these highly sophisticated pathogenic weapons, a single human on a planet is enough to warrant that entire planet being quarantined. Because even if the human and the entire area around them is vaporized the risk of even a single airborne pathogen escaping and finding a host is simply too great.
If a single alien aboard one of their colony ships is revealed to be infected the alien fleet hunts down and vaporizes that ship, the entire ship and everyone aboard it, there is an absolute zero tolerance policy, anything less would be insufficient.
The aliens could destroy us, send Earth into the sun, but they don't because they covet our immunity to their most powerful weapon, they want that immunity for themselves, with it they could conquer the universe by making every world inhospitable to any life but their own, as we could if we had their interstellar technology.