Could the human proteins come off the intestinal walls as the food traveled through the body? Have they done DNA studies? If cannibalism there should be DNA from both the eater and the eaten.
If you are referring to cannibalism as an “ancient way of life” are you thinking of the Aztecs or earlier groups? The Aztecs had only been city dwellers for a few centuries. The Toltecs were far more ancient, but I don’t know their practices. The Mayans were far older and did engage in human sacrifice, but I don’t remember cannibalism being a significant part of it. They often threw their sacrifices into sacred wells, sinkholes known as cenotes. Hard to eat them down 80 feet below the surface.
Here’s an article about the evidence for cannibalism as a way of life from the Olmec (1000 BC) down thru the Toltecs and Mayas to the Aztecs. The Aztecs invented little in MesoAmerican civilization. Much as the Romans with the Greeks, they largely elaborated on and carried to their logical conclusion earlier trends and practices.
We tend to forget that MesoAmerican civilization was around 3000 years old when the Aztecs showed up.
http://www.heretical.com/cannibal/mamerica.html
Here’s a (somewhat fanciful) article about the evidence for Anasazi cannibalism.
http://www.canadafreepress.com/index.php/article/45644
The author posits an invasion and conquest of the Anasazi by Toltecs, which due to distance and logistics is a little silly.
Although we have actual written and physical evidence of a Toltec army conquering a Mayan city, which was something like half or a third the distance to the US Four Corners.