Are there any non-terrible ways of storing secret keys for Google App Engine? Or, at least, less terrible than checking them into source control?
In the meantime, Google added a Key Management Service: https://cloud.google.com/kms/
You could use it to encrypt your secrets before storing them in a database, or store them in source control encrypted. Only people with both 'decrypt' access to KMS and to your secrets would be able to use them.
The fact remains that people who can deploy code will always be able to get to your secrets (assuming your GAE app needs to be able to use the secrets), but there's no way around that as far as I can think of.