The problem of killing bacteria, as I see it, will increasingly become something akin to the demarcation problem of philosophy. Why would it not be? It is natural that the optimal situation for pathogenic bacteria to be in is one in which they are indistinguishable from necessary cells. It may take an extraordinarily long time, but until we are able to completely eradicate a pathogenic bacteria
from the earth, we will remain in that arms race.
Humans are creative at killing bacteria, though it's already not difficult to "annihilate them at will". It's much harder to annihilate only the ones we don't like, only the ones that harm us, and only the ones that pose the greatest risk.