Was Mark Prior's downfall the fault of Dusty Baker, or incompetent doctors?

As someone who has nervously watched Phil Hughes' young career slowly begin to mirror that of Mark Prior, a pitcher with similar mechanics who was also promoted too early, I was somewhat relieved to find this article on Cubs f/x blog on the startling revelations of Prior's shoulder surgery once he was in the hands of Padres doctors:

If that weren't enough to put an end to his bid to pitch this season, doctors also found a second injury -- one that isn't normally associated with baseball.

Prior's anterior capsule was torn away from the humerus, the bone in the upper arm. Team physicians Heinz Hoenecke and Jan Fronek performed the surgery and said the second injury is normally associated with traumatic events like a fall.

The Cubs f/x blog noted that Prior fell on his right shoulder after a collision with Marcus Giles on July 11, 2003. While Prior's downfall is generally blamed on being overused by Dusty Baker, a manager who wouldn't read Moneyball if it had magical insulation powers during winter, it seems that this may have been the problem of clueless doctors more than any baseball decision. The numbers may actually back up that theory. Here are Mark Prior's innings totals from 2000-2003, the years he was healthy and dominant:

2000: 129.0
2001: 138.0
2002: 167.2
2003: 211.1

While the jump of 43.2 IP from 02-03 is slightly over the usual 40 IP increase that has a history of resulting in arm injuries, it's not really all that drastic, especially considering how good Prior's mechanics were, and that his major injury problem in 2004 was an unrelated Achilles injury. It would, however, explain his poor performance even when he was conceivably healthy.

This makes me feel slightly better about the chances of Phil Franchise.

(H/t: Baseball Musings)