You definitely don't want to check secrets into the repo for the same reason you don't set them as environment variables: It's not secure. The solution is to use Cloud Key Management Service. More info here: https://cloud.google.com/kms/ We use that to either store secrets directly, or to decrypt encrypted entities in a DB (e.g. Datastore).
You can see how we use it here (our project is open source): https://github.com/google/nomulus/tree/master/java/google/re...
Shows how to encrypt env vars with Cloud KMS then decrypt them in memory.
The reason being that these secrets are absolutely essential for many tasks that our registry needs to perform, and the past six years of experience have shown us that Datastore has better availability than GCS. We haven't seen Datastore ever go down unless all of Cloud is down too, whereas we have seen outages isolated to just GCS. Datastore also has lower latency (since it's a DB, not bulk file storage).
One caveat is that the maximum size of a single entity in Datastore is 1 MB -- if you're encrypting stuff larger than that then you'll need to shard (ugly) or just use GCS. Since none of our secrets are anything close to that large, it works just fine.