I’ve been wondering - wouldn’t rather a lot of the remains have burned afterwards? The heat was producing smoke for weeks - in fact, I’ve heard there are still occasional flare-ups.
Yep, I read the entire article. I also read the OP, which was entirely about bacteria and short-term health risks. Those who live by the terse link-with-no-explanation die by it as well. 
Does dead rotting stuff usually cause disease? More specifically, does dead rotting stuff cause epidemic infectious diseases that you mention?
Well, no…a dead body is a feast for microbes and for worms but is a less of a vector for infectious agents than a live human being–think typhoid Mary, Agent Zero, that kid with the sniffles sitting next to you. Putrefaction does not generate the bacterial pathogens you mention–biologists no longer subscribe to theories of spontaneous generation, miasma, or foul vapors. Cholera epidemics, such as the one in London outbreak of 1854, are caused by the (infectious) fecal contamination of water supply. This actually may happen in disaster stricken areas where safe water supplies are compromised, however, NYC probably has ample water purity monitoring and a redundant network making this disease highly unlikely. Plague is caused by Yersina pestis, typically carried by fleas and rats…trust me, there are LESS rats in New York after Sept 11.
Moreover, what we have at the WTC is essentially a large graveyard, and while the bodies are not embalmed and may well putrefy, they have been effectively interred. From a public health standpoint, the aerosolization of industrial/structural materials is more of a concern as is continuing smoldering fires. Burning plastics generate a lot of toxic hydrocarbons and nitrogenous compounds. Contamination of water with these pollutants is another bugbear to keep you awake at night.
Hope that answers the OP.
I have been wondering about this myself.
Not so much the disease angle, but, the umm, body count angle.
What do you do if you find a finger nail or something, suspend operations?
I imagine all recovered pieces are being saved for DNA tests, but I doubt there is much fanfare at this point.
Hopefully, the fires after the collapse consumed some of this material. Can’t even believe I just said that. But what are ya gonna do? There are still hot spots of 1000F. So I heard yesterday.
God, what a mess. The people doing this job will never be the same. I guess none of us will be.