Seems it was pretty common to know that sickness and shit would be deadly inside the body. From the same article:
"During the 4th century BC Scythian archers tipped their arrow tips with snake venom, human blood, and animal feces to cause wounds to become infected..."
Granted, they were trying a bit of everything, and Europeans did do things like use cowshit to build homes. (No, seriously--watch Tony Robinson's WORST JOBS IN HISTORY, which if nothing else, shows that shit was apparently quite important back then) But it doesn't take science to know that shit is foul, and that foul things might cause harm. I never said(that was Ellis) that they knew WHY.
An example that might illustrate what I'm saying here: Bleeding has, in certain specific cases, health benefits. As they didn't know why, though, they used it for most everything, and unsurprisingly most of the uses they put it to were inappropriate.
As Ellis lurks here, I really wish he'd settle this by explaining what his source is on that fact.