There are many bacteria and parasites that infest the fly, making flies a major factor in spreading many diseases by touching surfaces with their legs or their saliva. After walking on much excrement, flies may carry up to as many as 6 million bacterias on their feet. SO BE WARY OF FOODS THAT HAVE BEEN TOUCHED BY A FLY! Here's some information on the diseases some flies are known to help spread. (Source: http://library.thinkquest.org/C0117442/html/diseases.html; emphasis mine)

Even if there should exist such a disease that is only carried on one wing of a fly, and the antidote always coming on the other wing (any scientist of bacteriology will reject such a theory as impossible), what about all the other diseases on the feet of the fly? Why is Muhammad talking about the wings, when the main source of infection are the feet of flies?

Why is Muhammad making sure with his instruction that the fly gets a full body ablution in your drink, transfering the maximum number of bacteria and diseases into it?

Another website has this to say about flies:

... The two-winged flies constitute a larger order of insects and well over 110,000 different species are known throughout the world. This group forms one of the most highly specialized of insect orders and many species are of the utmost significance in regard to human welfare. If there is anything as "harmless as a fly", it is certainly not the common housefly or any of its relatives.

Diseases, e.g., malaria, dysentery, sleeping sickness, onchocerciasis, elephantiasis and yellow fever are carried or transmitted from man to man by bloodsucking dipterous flies. Many other diseases are transmitted mechanically by flies due to the habit exhibited by many species of sucking liquid from excreta and other decaying organic matter and then settling on and vomiting on your food.

The fly was made to distribute quantities of pathogenic disease organisms. Its 6 feet are equipped with bristles and sticky pads and its proboscis is hairy. A sticky liquid comes out of the hollow hairs on their feet allowing them to walk upside down and on glass, etc. The fly's digestive tract is an incubator for germs! My mother began to teach me IPM control when I was a very young boy. She said, "Shut the door you are letting in the flies!" This is still good advice - even better is to have a second entry door as an extra barrier against fly invasion.

... A well fed fly defecates at least once every 5 minutes!

(Source: http://www.thebestcontrol.com/bugstop/control_flies.htm; bold emphasis theirs, underline emphasis mine)

No doubt, the stress put on a fly by drowning it, would only cause it to vomit and defecate even more, releasing an extra portion of germs into your drink!

The first of the above links provides an even more detailed list of diseases that are transmitted by flies:

Leishmaniasis

This disease is found in South America, Africa, Indian Subcontinent and Europe.
It's caused by a parasitic protozoan transmitted by the bite of sand flies.
Symptoms of this disease usually includes fever, weakness, swollen spleen, and skin sores.
There is no treatment for this disease; it eats away at your skin.

Onchocerciasis

Onchocerciasis, also known as River Blindness is an infectious cause of blindness.
It is carried by a minute nematode worm that is spread by the Simulium black fly.
Found in South America and Africa, a bite from this insect can transmit the worm to its victim.
The drug invermectin has helped stop the progress of the disease.

African Trypanosomiasis

This is a sleeping sickness and epidemic caused by a protozan blood parasite Trypanosoma.
It is transmitted by the salivary glands of infected Tsetse flies in Africa.
Symptoms include a boil- like sore at the site of the bite, fever, headaches, and severe illness.
Treatment should apply in the early stages of the disease by anti-parasitic drugs.

Bartonellosis

Found in South America, this disease is caused by the rickettsia organism transmitted by the bite of a Sand Fly.
Victims are usually exhausted from anemia, and experience a high fever and wart-like eruptions on the skin.
Treatment is available.

Myiasis

This disease occurs mostly on animals such as dogs and sheep and cows, but sometimes it may occur on humans, more frequently carried by the Cheese Skipper fly.
It is transmitted by a fly that lays its eggs on the skin of another organism. The larvae can burrow into the skin or penetrate itself in open wounds.
Symptoms include violent abdominal pain, nausea, vomiting, and diarrhea with bloody discharge.
There is currently no treatment for this disease (on humans, that is; on animals insecticides are used), except to either let the larvae grow and leave at its own accord, or to remove it by enticing it.

Typhoid

Flies rummaging around excrement may come across bacteria known as Salmonella Typhi, which may come from a person shedding it.
This disease is a type of fever. Symptoms include a body temperature of as high as 103° to 104° F (39° to 40° C), weakness, stomach pains, headaches, and/or loss of appetite.
This disease can be found all over the world except in industrial countries such as United States, Western Europe, and Japan.
Treated with the drug chloromycetin, or ampicillin for those infected with bacteria that is immuned chloromycetin.

Dysentery

This is a chronic disease that affects the large intestine in humans.
The parasite Entamoeba histolytica is the cause of this disease. This particular parasite can be found in uncooked meats, and may be transported by flies.
This disease is characteristic of severe diarrhea and severe stomach cramps.
Treatment with drugs containing metronidazole or ementine is recommended.

Leprosy

Leprosy, also known as Hansen's Disease, is a chronic disease that affects mainly the skin.
It is caused by the bacillus Mycobacterium leprae, which may be carried by flies from rotted foods.
An early symptom is anesthesia (or the numbness) of a patch of skin. Some muscles may be paralyzed. Because of the numbness of some nerves, injuries to the area are not noticed.
This disease is generally rare nowadays, but that doesn't mean it doesn't exist. A vaccine for leprosy is currently being developed.

Qur'an, Islam & Science
Answering Islam Home Page