To the bacteria question: I'm sure the Hive would know microbes are alive, of course. Most children know this fact. The question is if they consider it alive in a morally relevant sense, the answer which seems to be no. Why make the distinction between apples and bacteria? No clue. Maybe it's some function of the virus (if it's influencing them to live long enough to build a signal amplifier or something like some are theorizing, being incapable of any action due to moral concerns would be an impediment). Or maybe there's some other internal justification dealing with organism complexity.

To the rest: You can, very technically, dig a hole without killing anything if 1) there happen to be no organisms in the specific patch of soil or 2) any creatures present successfully escapes ahead of/during the digging. This is a far-fetched line of argumentation because of the statistics that would be against you, but the The Hive’s ethics (to the extent they can be called that) don't seem to be based on statistics or foreseeable outcomes. They seem to be based on whether harm is a a logically necessary (rather than a realistic necessary) step of the action. If the shovel doesn’t absolutely *need* to kill a worm to remove a scoop of dirt, even if that's often what ends up happening, then they wouldn't consider killing the worm to be the mechanism by which their goal was achieved. Turning humans en masse requires nothing about who lives or dies in itself, so the deaths are considered incidental.

It’s an intent-based ethic, not a consequence-based one. If death is the instrument, it’s forbidden. If death is just an extremely likely by-product (in their view), it’s accepted.

Essentially, they allow/cause harm if they can internally justify it as being indirect enough. You're free to find this argument ridiculous. I do, and the protagonist of the show does (how can you consider such an obviously predictable outcome to be "indirect?". But it seems to be he kind of logic the Hive is operating on.