"Incineration is possible, but it isn't as easy as burning the carcass in a fire. Temperatures of more than 1,100 degrees Fahrenheit — sometimes up to 1,800 degrees — are required to effectively neutralize prions. Unlike most bacteria, regular cooking won't help at all. "Disposal issues are tough," says Barbara Powers, director of Colorado State University's Veterinary Diagnostic Laboratory."
You need about 20 minutes, a pressurized autoclave, and some nasty chemicals to do this effectively. There is research into other methods but I really don't know anything about them.
The only reliable method that I'm aware of to denature proteins without making the whole thing inedible is hydrolysis. Gelatin is made from collagen in the skin, bones, and connective tissues of various animals, but Jell-O is generally considered safe.
"Protein" in food really means "amino acids" as far as nutrition is concerned; even if the protein isn't denatured by cooking (and at least some proteins are), it will be broken down to amino acids by your digestive system before being absorbed into your body. Your body uses the amino acids to build its own proteins.
http://www.ncbi.nlm.nih.gov/books/NBK22600/
"Proteins ingested in the diet are digested into amino acids or small peptides that can be absorbed by the intestine and transported in the blood."
If by "animal-source protein strings" you mean "small peptides", then yes. But in general they still have to be resynthesized into the proteins used by the body. There might be a few useful proteins that are small enough to fall into the "small peptide" range and would therefore be absorbed and used as-is.
Prions have a little over 200 amino acids, so they are on the large side to be considered "small peptides" (which AFAIK are typically a few to a couple of dozen amino acids). They appear to be resistant to the enzymes that normally digest proteins, and it doesn't appear to be clearly understood how they get from the digestive tract into the bloodstream. See, for example, here: