Is is possible to keep the pup away from the rocks? You probably have already tried that...
Is there a possibility of spraying these tempting rocks with a bitter apple spray or something safe, yet intolerable to the pup, so the next rock encounter would not be pleasant?
I agree with Invincible and the idea of adding minerals to the diet. Sounds like you are doing well with the raw food plan. I look around for the best deals on raw meats which keeps the costs way down. I personally find it is cheaper to feed raw than commercial dog. As the puppy grows you will feed more, but then once they acieve full size, the amount of raw food needed for maintenance will actually decrease and settle down, unless the dog is working strenuously.
Invincible taught me about EFT for animals. It might be an idea for this.