Crushing the capsule in mouth is not harmful to cats. But it greatly reduces the benefit of the medicine.
Azodyl capsules are refrigerated to keep moisture intact and prevent heating. Otherwise the bacteria will die. And the capsule is meant to keep the bacteria together until it reaches the intestine where finally the capsule dissolves and bacteria is released. If taken in crushed form, most bacteria won't reach the intestine.
If you want your cat healthy and your cat is not buying pill pocket there is no other alternative but to force feed.
Depending on whether your cat likes fish or chicken you should prepare fish or chicken soup. You should keep a syringe ready. Then you have to hold your cat in such a way that his nose points at ceiling. If your cat is not docile enough you have to take the help of another person.
Then open the cats mouth and quickly puf the capsule in her mouth and push it as back in the mouth as possible. Then close the the mouth and hold it so that the cat is not able to open the mouth. Rub the cat's throat to encourage him to swallow the capsule. There is gap in between front teeth and back teeth of cat. Use it to insert the syringe and push in the chicken or fish soup. It is to ensure that the capsule does not remain stuck in oesophagus and reaches stomach.
Hope this helps.