When you break down the process of having a private company comply with an order to create a particular piece of software, there's many failure points.
The counter from the governmental side is "we will give your company massive fines until and unless your company complies".
As a note, the actual text of the court order (https://www.documentcloud.org/documents/2714001-SB-Shooter-O...) explicitly says that Apple can appeal it on grounds that it is an unreasonable request. Uncooperative engineers can make it an unreasonable request, and have the legal right to be as uncooperative as they want to be in this case. And, they're on the same side as the CEO of Apple ethically, so it isn't career suicide.