"I think it's inevitable," Michael Hill, president of baseball operations, said. "He has to have surgery. It's just a matter of when he comes to grips ... and makes that decision."
On Tuesday night the team announced the severity of Fernandez's injury. Surgery was recommended, and the 21-year-old is expected to miss 12 to 18 months.
The injury to the 2013 National League Rookie of the Year has become one of the major story lines in the Majors.
Though only in his second season, Fernandez has already captured the imagination of many. He was off to a strong start, having been named NL Pitcher of the Month for April.
"Like all of us, we're fans of the game," Hill said. "So we appreciate and respect the game, and have a passion. When you see somebody who embodies that passion, you want to root for him. Jose enjoys what he's doing -- not just every fifth day, but every day he was at the ballpark, he had fun with his teammates. Now he's going to have to do it in a different capacity for the next 12 or so months."