Edit:
You were using Circleci Contexts, so with that you had a set of secrets of each env. I know they are working to bring secrets to org level, and maybe team level... there is no info if they will create sort of contexts like we have in CCI.
I have thought on adding the env as prefix of the secret name like STAGE_GITHUB_KEY or INTEGRATION_GITHUB_KEY using ${env}_GITHUB_KEY on the yml as a workaround for now... What do you think?
--- Original answer:
If I understand you well, you already have the dotenv files stored somewhere and you want to inject all those secrets into the steps, without having to manually add them to github secrets and do the mapping in each workflow you migrate... right?
There is an action made by someone that reads a dotenv file and put its values into ouputs, so you can use them linked in further steps. Here is the link: https://github.com/marketplace/actions/dotenv-action
Whatever is present in the .env file will be converted into an output variable. For example .env file with content:
VERSION=1.0
AUTHOR=Mickey Mouse
You do:
id: dotenv
uses: ./.github/actions/dotenv-action
Then later you can refer to the alpine version like this ${{ steps.dotenv.outputs.version }}