First and foremost, I should say that I don't trust 99% of doctors when they talk about nutrition. I've heard no less than four PHD's with backgrounds in biochemistry, sports science, nutrition, etc state that hospital and general medical recommendations are worthless. They all had to do a stint as part of getting their PHD's, hence the great disdain.
Now in respect to someone already going through renal failure, it is true that protein is problematic as you say. However, one of the few things Lowery did say about his book was that, in a massive review of modern literature, he found nothing to indicate that high levels of protein directly stressed the kidneys. Now, he didn't say what the tested ceiling was on any of these studies, but since ketogenic diets push well over 300-400 grams of protein per day with no reported kidney risks. I listened to an interview with the foremost researcher of ketogenic diets and recall her saying no such risks have come up.
Kidney stones, of course, may be another matter entirely. High protein, calcium, and caffeine intake can contribute to these, from what little I have heard on the matter. This is something to watch out for if you are thinking of a seriously high protein diet.
I should also point out that the kidneys are organs that have corresponding adaptive capabilities. This means that appropriate stresses will likely be beneficial to their function, or at least produce adaptations rather than causing failure. For example, a small intake of alcohol on a regular basis results in stronger kidneys, as per clinical studies. One theory is that our kidneys are adapted to filter out a much high amount of toxins from the Paleolithic era, and that the work of breaking down alcohol exercises them in the same way that cardiovascular activity stresses the heart.http://www.amazon.com/Dietary-Protein-Resistance-Exercise-Michael/dp/1439844569
Lowery knows his shit and is a highly-respected researcher. Granted, I have an extremely high standard for meta-analyses that he hasn't quite been able to match during his online radio shows (Iron Radio) but he still displays an encyclopedic knowledge on the fly. I'm sure that, with time to sit down and write out his thoughts, he's produced a top-quality product. I have a number of other books on top of my list first, but this one makes sense for anyone contemplating long-term high-protein diets.
Carl Lancone (Superhuman Training radio) is another guy worth looking up. He's all about nutrition, supplements, etc, and has fuck tons of ads on his show, but he really knows nutrition. His appearance on Iron Radio was a back and forth of studies, nutritional info, etc with Lowery that really impressed me. He may have some things to say on the questions you've raised - I'd recommend checking out both the IronRadio and the SuperHumanTraining rss feeds to search through old shows that might be relevant to your questions.