Two parts to this issue. First, was the hurt player playing better than his replacement? That's a judgment call by the coach. Second, is the hurt player risking further injury by playing? Although the player has input, that's a call by the team doctors and trainers. Shanahan did not force (or even allow) a player who was, by doctor's opinion, at greater risk of serious injury. Would a healthy Cousins, allowed to perform more than a couple of closing series, been better positioned to win the game? I'm not sure, but that is the only part of this situation that applies to Shanahan, not the subsequent, more serious injury.
RTR,
Tim