While I agree the Red Sox want to protect their investments, you're assuming that the injuries stem from overuse. There is no evidence behind that. Beckett had back problems last year and before that had no prior history of any major arm troubles. Much like you're inferring that you can't take results and attribute them directly from an action in this case:
You can't infer that Beckett was ineffective as a direct result of being left out there too long in his last start. While it may be true, you can't state as a fact it is. It's an easy excuse for him to use, but you never heard it out of his mouth, or anyone else's. You're also infering that "arm soreness" is something unusual. Every pitcher who throws 100+ pitches many of them 95 mph has arm soreness after a game. Why do you think they wrap themselves up?