As I wrote above, I am not 100% convinced that bacteria or pathogen on the fly would be a cause either.
You have to remember that bacteria is the almost perfect example of "survival of the fittest". In that only the bacteria that are best adapted to each specific environment (temperature and available resources the biggies all covered under the umbrella of "environment") will become dominant and push the others out.
So, the bacteria that would be dominant on any dung or rotting material that the fly may have visited, would be the bacteria that is best adapted toward living on dung or rotting matter, in the air, at the temperature and humidity of the ambient atmosphere.
If that bacteria were suddenly introduced to a very different environment, in all likelihood it would not survive. That is, bacteria that is adapted to live on rotting matter in the air probably will not survive in a liquid environment without rotting matter.
Furthermore, the bacteria that is well adapted to live in an aquatic environment, would in all likelihood be able to out-compete the bacteria that is not well-adapted to the new environment. And, all of our tanks that have been established for more than 2 or 3 weeks have a very rich bacterial environment. It is all covered under the broad topic of biofilm. The biofilm bacteria are going to outcompete the non-adapted bacteria for any resources in the water column, simply because the tank bacteria are better suited to that environment.
Furthermore furthermore, this bacteria -- that I don't think stands a very good chance of surviving anyway because of the above -- would then have to be deleterious to the fish. In the same line of argument as above, why would bacteria that is well adapted to consuming rotting matter (or dung or whatever) be good at attacking fish? That is bacteria that is best at consuming dead or decaying or fecal matter, not healthy living matter.
For that matter, unless the fish were under some sort of significant stress, why wouldn't their immune systems be able to fight off whatever tiny amount of bacteria that was introduced into the tank?
For fish to become ill, they have to be attacked by a fish-specific pathogen. That is, a bacteria or virus or protozoa or whatever that is adapted to specifically attach fish. The best example is probably ich. Ich has to have fish to parasitize off of, otherwise it cannot survive. The vast majority of diseases that infect our tanks are caused by pathogens that are fish-specific. The few exceptions are usually only good at infecting a few extra species. A good example of this is the tuberculosis (TB) that fish can get. It isn't the TB that can infect humans very well. In the vast majority of cases, if you catch TB from your fish, you get a small sore that goes away pretty quick and that's it. You don't get the dangerous TB because the organism that is adapted to giving fish TB is poorly adapted to give humans TB.
I'm not saying it is impossible, I am just saying that I don't think that it is very probable. A healthy tank should not have succumbed to any tiny amount of foreign pathogens that may have been introduced to the tank. The introduced bacteria, coming from an environment in air aren't likely to have taken well to living in an aqueous environment. The bacteria that is well-adapted to living in the tank would have in all probability squeezed out the poorly-adapted introduced bacteria. And, if the fish had healthy immune systems, they should have been able to fight off a small number of pathogens.