I'm sure the CWS didn't think he was going to be Cy Young this year. He wanted to start, and they let him start after being only used as a reliever. I don't think they could have imagined he was going to be this good as a starter.
I don't think there are many instances of teams investing a ton in a player, even one not coming back from injury, and then throwing their arm off the same year they acquired him. CWS have the luxury of shelving him and still remaining the worst team in MLB, no pressure there. They don't have to trade him, if he gets through the season healthy, he'll be worth a lot more in the off-season.