Jim, if whey protein becomes denatured it will not change the fact it, same as all other proteins, contains cysteine. Your digestive system (not just the stomach) will convert all proteins into their constituent amino acids - these, including cysteine, can be transported into the blood - cysteine can then, among other things, be used to make glutathione.

In general, whole proteins can not cross the gut (stomach, etc) wall into the blood unless something has gone wrong.

What the gut does is to break down large molecule into their small components (amino acids in the case of proteins, sugars in the case of polysaccharides like starch, etc). These small components are transported into the blood where they are used for many functions.