Will I be medically discharged for severely low Vitamin D and severe stress fractures?

Since the Army is already putting a lot of money into you, they are waiting to see if you can heal up enough to continue training. When I went to my first AIT, there was a guy that was a medical hold over. Had been a medical hold over for at least six months because he had crushed his hand. How, I don't know, but it was crushed pretty bad. He was cleared to train right before my cycle started. Could he have been medically discharged...possibly....but again, the Army put some serious money and time into his medical treatment. I'm guessing this is what is going on with you. You got hurt on the Army's time, therefore your treatment is on their dime. Perhaps at the end of the 9 months, they will re-evaluate your situation to see if you need to be medically discharged.

In the mean time, get healed up, and enjoy the next 9 months of Active Duty pay.

You just stated that they told you it would be 9 months before you could start class again. That does not sound like they are planning on discharging you. If you have questions, why are you asking them here instead of where you should; your doctor.

When the VA told me my Vitamin D levels were low, they had me go to Wal-Mart and get the Vitamin D supplements - little gel pills. Basically, you get deficient of Vitamin D if you don't spend enough time in the sun.