I don’t think for the court it was an issue of making wise policy choices but of who had what authority, and what did the law say about it. The court simply didn’t have anything enabling them to delegate their powers in the Chevron case.
The separation of powers is core to the structure of our government, delegating powers onto other branches nullifies that. Hence the non delegation doctrine. Perhaps it [Chevron] may be good policy but it simply isn’t how our government is structured.