Who's to say that the bacteria, viruses etc on all these alternate Earth's are the same as on Datum Earth? There could be much more deadly versions of disease out there than on Datum Earth. Although there are a lot of animals that are different on other Earths, there are those which seem quite similar and could potentially harbour disease that other animals aren't adapted for. Even in real life, there are problems with disease moving from one species to another, because the second species hasn't adapted to it (e.g. bird, swine flu).
Potentially, stepping between these Earths could rapidly spread deadly disease that the plants, animals etc in each Earth cannot cope with and destroy the ecosystem.
The Long War indicates that it's not quite so bad. That is, while there are new deadly diseases to be found in the Long Earth (Earth West 141,759 is a Joker because it has some particularly virulent plague), thus far it has been kept relatively contained — there certainly hasn't been any rapid spread, it being decades after mass human stepping without wide-spread disease-caused ecosystem collapse.