While in this case protein is just generic for 'meat', in the specific cast Tyson is taking plant protein that you or I cannot consume and turning it into a protein that we can eat. Does an oil refinery destroy oil? Well, I guess so, but that is not exactly the term that is commonly used to describe the refining process.

It wasn't clear to me that "protein" was generic for "meat", but in this specific case soybeans can be turned into tofu. And that's a reasonably popular protein source for humans in China -- especially if high prices of other human-consumed proteins causes product substitution.

They produce more protein than they consume. The animals convert carbohydrate to amino acids (well, the bacteria in their gut does).

You seem to have forgotten https://en.wikipedia.org/wiki/Feed_conversion_ratio#Pigs ?

They have nitrogen-fixing gut bacteria now?

No, the bacteria in the rumen convert amino acids that cows and humans can’t digest (and hence are of no nutritional value), into amino acids they can digest.[1]

Thus, they are net producers of useful amino acids.

[1] http://www.publish.csiro.au/ebook/chapter/SA0501041