Ok.
Barring factors out of our control, and assuming we trust the supplier and their supplier, and also assuming the company follows the law regardless of how lax it is (completely ignoring why a company would risk getting customers sick with unpasteurized whey (as you implied two companies do)), the question that we are attempting to answer on some level is whether or not it matters if the protein is denatured during the pasteurization process.
To address that, I've read before about the particular way whole proteins are unfolded by our digestive tract. I couldn't find much of anything from an acceptable source, but I ripped this from another forum because the guy sums it up really well.
First, whey proteins can be derived in two ways 1) as a bi-product of the cheese making process, and 2) directly from skim milk in a process of extraction of micellar casein (native whey processing).
Second, whey protein can be denatured outside of your body and inside of your body. There are two processes that can eventually denature whey outside your body: 1)pasteurization - two times during the cheese making process, and 2) and by adding of citric acid to whey after it has been separated from the curd (both of these are in the cheese making. When whey is made from skim milk direclty there is only one pasteurization and no acidification).
Studies (can't post links yet otherwise I'd provide the links to the research papers) show that pasteurization denatures whey only partially (when milk is heated to 72C/162F). Both beta-lactoglobulin, alpha-lactalbumin can make it trough this process. Beta-lactoglobulin is more susceptible to damage, but it happens at higher temperatures.
What can damage these native fractions is low PH. In cheese making PH can go as low as 4.0 and even lower. At this point the native fractions suffer damage, but what really renders them denatured is the addition of citric acid later in the processing of whey. The PH goes to 3.0.
Now, you say, if PH of 3.0 will denature whey, what happens in the human stomach where the PH can range from 1.0 to 3.0? Well, it took me literally 3 days of digging trough all available research papers, but it seems the body actually must break down the native fractions to other smaller peptides that actually exhibit the health benefits associated with them (apart from the immune-boosting properties of cysteine-cystine to glutathione - these exist in both undenatured and denatured whey but the ratio is different - more cystine in the denatured).
So, it works like this: native whey fractions enter the stomach, the stomach recognizes them for what they are and it secrets the right amounts of the proteolitic enzymes pepsin, trypsin and chymotrypsin. They unfold the peptides to the right forms of smaller peptides that act in a positive, health supporting way in the body. It's like a key lock and a key that fits perfectly in it. This doesn't happen when the whey fractions are denatured. The enzymes still break them down into smaller peptides, but they are not the ones, associated with denatured whey and its properties. So, in effect the native whey fractions do not survive the low PH in the stomach unchanged, but are not destroyed/disabled either. In fact, one study demonstrated that one of these fractions - lactoferrin - can completely survive the action of the proteolitic juices and can move down the digestive tract intact.
In summary, you have to start with undenatured whey if you want the immune-boosting, anti-hypertensive, anti-oxidant, etc. properties of whey. Don't worry what happens in the body. The body knows how to deal with them in order to take advantage of their unique properties. On the other hand, if you start with denatured whey protein the body will still use it as smaller peptides and individual amino acids. It will also make glutathione from the cysteine amino acid regardless of the ratio cysteine-cystine (cystine simply takes one more step to convert to cysteine).