As I mentioned, Paleo is not necessarily a high-protein lifestyle. Even Atkins does not have to be a high-protein experience.
There's also the question of what is considered "high." For purposes of studies on this subject, I suspect protein levels are far higher than that practiced by people on Paleo or Atkins, which advocate up to 1.5 grams per lb of lean body weight at maximum, for highly active people, if i recall correctly. Without access to the data for the studies you quoted, I can't address how much protein, or what types of protein were being used. Nor can I gauge the integrity of the studies (are they real, clinical studies, or just questionnaires? What do the researchers consider "high"? What assumptions are they making, and what are they leaving out? etc.)
I do know that one of the earliest studies that sparked this whole fear of protein consumption and kidney damage was incredibly flawed, feeding people extremely high levels of incomplete proteins from low-quality protein concentrates, exclusively, with no fat. It was a recipe for disaster, people died, and it made the headlines, but it was completely unlike anything any human could ever achieve eating a diet of real, unprocessed foods.
There is evidence that very high protein diets may accelerate pre-existing kidney damage. Atkins admitted that. That's not really the same issue though. If studies show intense exercise can damage the hearts of recent heart attack victims, would we all suddenly start saying that pumping blood is bad for the heart, or exercise is bad for the heart? Of course not. One of the functions the kidneys were made for is processing protein, like the heart processes blood and the lungs process oxygen. Anything is harmful in extreme enough excess, or during injury, including exercise or hyperventilation, but the amount of protein advocated by mainstream Paleo promoters is hardly at that level.
I'm sorry to hear of your sister-in-law's kidney issues while on a higher protein diet. I was born with only one kidney and as such, have been monitored closely by my doctors since my early teens, and I'm very sensitive to the topic. Doing Atkins 10 years ago, and low-carb Paleo now, improved my markers of kidney function rather than worsened them. It also eliminated my non-alcoholic fatty liver disease and brought my blood pressure to normal levels, while my triglycerides plunged. N=1.