Sorry you're going through this with your baby, I know how difficult it is. Did she tell you what type of crystals/stones they are? The treatment is very different for each type. There's Calcium Oxylate and Struvite. Unfortunately, I have had to deal with both. Our senior Malamute developed the Calcium Oxylate, and the only treatment for those, unfortunately, is surgery. I wouldn't waste any time with it, if it is Oxylate stones/crystals. My boy, Thorin, had one that was very large and jagged, lodged in his tube and could have created a blockage, which is emergency time. Our vet said he must have been in excruciating pain, though the poor boy never showed it.
Our other Malamute, a 2.5 yr old has been dealing with Struvites for almost a year now. Those can be reduced/eliminated with diet. Struvites are often caused by a high PH. There is also medication to help reduce the PH in the urine, but I would try a diet change before giving any medication. But that's just me
I'm assuming that since your vet has already stated surgery, they are most likely Oxylate.
Good luck and let us know how your boy is doing!