The main problems of pathogenic (disease producing) bacteria via ingestion from insect contaminated water would be the ones they would transmit by their contact with contaminated materials. Flies (and other insects) that land and feed off of the contaminated pile of fecal mater and then land on food and/or water you are about to ingest can easily transmit enteric pathogens. However, in a true survival situation, where you cannot treat/boil the water, risking an intestinal bout would be preferable to dying from dehydration. Even if you drink contaminated water, your personal health, genetic background, number of organisms and a whole host of other factors will all determine if you become ill.

Pete