It's simple. Teams always think they can fix a guy's mechanics.
Only time will tell. I bet that they'll either handle him with the kid gloves for as much time as possible, or make the necessary adjustments as they go along, which if you had read what i posted thoroughly, would have noticed that's what happened with Smoltz when they lowered his arm angle.
By the way, your initial statement was that Dusty Baker ran Mark Prior to the ground, well consider the following:
It's not scientific analysis, but it makes sense.
Again, only time will tell. But hundreds upon hundreds of examples of kids who get hurt early due to poor pitching mechanics makes a hell of a lot of a sample size and logical explanation.