What advice should I give to someone who is receiving a Navy boot camp medical separation?

I think, my dear old sea salt, that there is more to the story.
I am extremely dubious that she is not receiving care or pain suppression.
I think you know this, though.
What is important for grandpa to do is be supportive, get enough details to give sound advice, and encourage her to heal and get back in the fight.
Do you have the means to pay her a visit? It might be illuminating.

My wife sort of went through the same thing last summer. She injured her ankle in Week 3 going into Week 4. After a few weeks of going back and forth, the doctors finally said she needed surgery. But prior to that they just had her in a walking boot and stuff. When it came time to decide on the surgery we had to make the call on if we wanted the Army to do it or to sign the AMA and just have her come home and we would get it done back home. Honestly, at first, I told her to get it done by the military but then when they said she would have to rehab in the barracks and we wouldn't be able to fly down to see her, I told her to sign the AMA. She came back home and we found out the doctors were not exactly spot on with their treatment. The doctor back here changed her diagnosis and 2 weeks after getting home she got a cyst removed from her ankle. The Army docs were saying she just sprained it. She spent 2 weeks after surgery not having the ability to walk or really do anything. Thankfully, my boss knew what was happening and I worked from home for two weeks to take care of her.

I guess that is the long way of me telling you the advice I would give her is to make sure she gets a copy of all her medical records BEFORE clearing. Then, go see a private medical professional within days of getting back. And the advice I would give you, which you probably already know, is to not talk down about her not completing training because of the injury. Be the supportive grandpa and just reminder that where one door closes, another opens.

Grandpa to Grandpa, I ran an Orthopaedic medical practice for eight years. While that certainly doesn't make me medically qualified in any way, I do know that once the bones are set, it's a waiting game. If she suffered some simple fractures, the docs may be just waiting for the bone to grow enough to make them confident she's OK to send home. Not minimizing your granddaughter's condition, but it is something like watching the grass grow once everything is set up. It's been ten years since any of my kids were active duty, their military medical care was excellent at the time.