The recommended solution is still vulnerable to employee compromise: if they can push software that runs as a trusted role, they can steal any secrets that software has access to.
This is certainly the case, however for an organization implementing best practices for code deployment, such a change would have to be peer-reviewed in the best case, or pushed directly to master with an obvious paper trail in the worst. It wasn't my intention to imply that employing well-designed envelope encryption would shut the door on any possibility of an engineer gaining access to secrets; clearly there's a lot more involved in making that happen. However, this goes a long way to allowing the source of any leaks to be traced should they occur.
Presumably, your rogue employee won't follow best practices, and there is not a quality audit trail for such abuse in most setups. I think we're in agreement: this is a hard problem and difficult to solve. In your article, that part of the problem statement is a red herring, as Cryptex doesn't solve it.