1) I am amazed at how many people think that JT (though I am optimistic he will serve the team well) who has just barely been able to unseat Jones for the back up role, is all of sudden going to become so good that we wouldn't welcome a healthy Braxton Miller back to lead the team next year. He is one of 4-5 guys who is a legit heisman candidate (and has been for 3 years), he isn't just some average player.
2) As to the question of whether he will come back healthy, well that is a different story. A labrum tear is not like an ACL, especially for a thrower. They can't go in and make that stronger than it was, a la Adrian Peterson. The joint will never be as stable. The labrum doesn't regenerate, and it doesn't heal if you try to repair it. So they will likely take out the torn part and hope for the best with rehab. There are some techniques to try and improve stability, but success depends on the type of injury and though he may recover to play again, maybe even as a QB, the likelihood he comes back at the level he was before is very small, probably under 20%, definitely under 50%.
That being said, I truly hope he beats the odds and I am ABSOLUTELY rooting for him, both for his sake and the sake or our team, because next year should be a much better squad all around than this one (which is about as "re-built" a team as you can get).
However, I think he might want to consider how he could be used as an "H" back, WR, or RB. It might also offer him a possible entry to the NFL, which I don't see happening now at QB, ever.