I just had the same experience with my dog earlier this year. I work at an animal hospital and got chided for feeding raw. The vet told me that if I wanted to feed natural I should feed canned. I envisioned a pack of wild dogs chasing a can...Anyway, she recommended c/d and I did feed a couple of cans more out of stressing out. She didn't really like it and her poops were big mounds.
Anyway, with struvite crystals, many times when you get rid of the UTI, the struvite crystals go away. Your dog can live with a few struvite crystals but once an infection starts, there is a risk of the crystals sticking together and stones can then form. I would finish the antibiotics and then get another urinalysis done to make sure the UTI is gone and there are no more crystals. I bought a supplement from Wysong called Biotic ph- which I added to my dog's food to help her urine become more acidic. You can try that until the crystals are gone. Also encourage your puppy to drink more water....add chicken broth (low sodium) to his food and/or water. Is he getting enough exercise? Inactivity may also contribute to crystals.
The foods that are meant for crystals, whether they are struvite or calcium oxylate, contain salt to encourage the animal to drink. I'm not a big fan of this especially if a dog has kidney problems.
Stick with your current food, just add water or broth or maybe try that supplement. Solid gold also sells a supplement called Berry Balance which is to prevent UTIs or maintain urinary tract health.
Give a dog food and make him prosperous, he will not bite you. That is the principal difference between a dog and man. (Mark Twain)