Um... did you change your username greene?
Protein in general can have a small net acid load on the blood regardless of whether it comes from plants or animals. This small net acid load can be easily offset by eating plenty of multi-colored vegetables. Remember, there are no carnivorous humans, only omnivores and, if you so choose, herbivores. So there is no excuse for anyone not to eat their vegetables. I get my fair share of veggies and then some and lift weights to boot, so I know my bones are solid and healthy.
It's not the diet itself that I find damaging, it's the way its spun, oversimplified, and marketed. It's the marketing that says eat whatever you want as long as its not carb. The diet itself, from the original source, teaches calorie restriction, which is the tried and true method for weight loss. But the huge Atkins brand that exists today consists of more of the same processed, nutritionally broken-down and reconstituted junk that groups like LeanCuisine have been putting out for years.
1) eat real food - more vegetables, moderate meat, moderate fruits, less grains, less sugar, less vegetable oils.
2) exercise - moderate intensity cardio, sprinting, heavy lifting, dedicated stretching and mobility.
3) live - relax, de-stress, meditate.
Disclaimer: I'm not professionally qualified to make any formal recommendations. I've just done my homework and I'm my own guinea pig. All of my data, unless otherwise cited, comes from a sample size of n=1 (me).