I've found this is largely solved by strictly separating plain config and secrets, and then having secrets pull from GCP secret manager / vault / whatever.
You can then commit all the config (including the secret identifiers) and it all just works so long as you're authenticated with your secret storage system.
We do this for the live configuration as well in line with Gitops and find it to work well.
If you don't want to use a cloud secret manager you can also use something like https://github.com/getsops/sops to commit the encrypted secrets safely