First off generally these diseases are limited by environmental conditions and available vectors. So starting with clean seed/stock can permanently eliminate the need to worry about many of the diseases. A good example of this is SQMV. It's spread mostly by the spotted cucumber beetles. These are only found in some states of the U.S. and Mexico.

As for how to deal with the disease depends completely on the pathogen. You can clean up many diseases by proper sanitation and crop rotation techniques. Historically leaving a field fallow was a method to reduce disease pressure.

Others are not so easy to get rid of. For example, Fusarium species can persist in the soil for up to 30 years. Once you get it, you are not getting rid of it. It's such a large issue that commercial growers in highly infected regions have gone to grafting resistant rootstock of a different species.