The headline here is that there's no reason to believe "environment variables" were the reason this data was breached; presumably, the database those variables came from was what actually got hit.
These problems were all solved a long time ago.
We have a couple of VMs that are not mission critical, and they don't hold sensitive data. We just inject the secrets into the runtime. Access to those machines is restricted to a single IP, there's not much more protection in front of them.
A meaningful attack on one of those machines would require a LOT of effort, and almost nothing in return. Some systems don't NEED to have government level security, as a developer it's my job to provide the best solution for each scenario.
(IE, I wouldn't put 12 security cameras and an armed guard around a fruit stand, but I might around a jewelry store)
I'm not sure I get the difference - the issue I would have thought was having the system code have access to the secrets themselves? Env file vs env vars injected at runtime seems the same there - either can be exfiltrated. The difference would be having it injected when used.
Is the problem with files about what happens outside that, being committed, etc?