I'm the creator of Node dotenv and I gave this a lot of thought a couple years back. I put together a whitepaper on this. Ultimately your secrets do still have to hit your environment. But at-rest they should be split from the environment. Today I think that is encrypting your .env file and keeping the decryption key separate. Bring the decryption key only at runtime inside your environment.
https://dotenvx.com/whitepaper.pdf