If the Yankees announced today that Ellsbury was retiring but would be come a base running coach/consultant for $35 million (about what they still owe him) for, oh, the next 10 years, everyone here would be screaming bloody murder.
The Red Sox and Pedroia signed a contract and each has to live up to the terms of the contract. The Sox have to pay him, and Pedey has to try and do whatever it takes to be able to take the field, even if he physically can't. There is no way around it unless Pedroia voluntarily walks away.