Some people have dairy alergies and some of those alergens are passed on through whey. You have to be ultra sensitive for that to be an issue though. I remeber Peter DelOrto talking about that once. I think he went with a pea based formula.
Some people take just protein shakes in an effort to minimize body fat. In this case, the hazzard is missing nutrients you should get from whole foods. This isn't really a negative factor of the protein though. The article was talking about 2-300 grams of protein in a shake. This must be what they are thinking of since this is an unrealistic amount to take for any other reason.
Ketosis is not dangerous and is a result of low carbs, not protein by itself.
Kidney stones have several contributing factors, reasonable levels of protein are not one of them.
Soy may very well have side effects. I can think of others besides those listed.
Over all, I wouldn't worry about it if you use it reasonably and have no obvious issues.Side issue - Kidney Stones: http://en.wikipedia.org/wiki/Kidney_stone#Prevention
...A positive association between animal protein consumption and recurrence of kidney stones has been shown in men, but not yet in women...
Any time an association is made for one sex but not the other, and there is no good reason for it, it's probably a spurious association.