A variation on query whitelisting is query signing.
During the build process, each query is cryptographically signed using a secret which is shared with the server but not bundled with the client. Then at runtime the server can validate that a query is genuine.
The advantage over whitelisting is that writing queries in the client doesn't require any changes to the server. This is especially valuable if multiple clients access the same server (e.g. web, desktop and mobile apps).
Example
In development, you write your queries as usual against your dev server which allows unsigned queries.
Then in your client build step in CI, each query is tagged with its cryptographic signature. This signature is sent by the client as a header to the server when making the request, along with the full GraphQL query string.
Your staging and production servers are configured to require a signed queries. They calculate the signature of the query received in the same way as the CI server did during the build. If the signatures don't match then they don't process the query.
Limitations:
- not suitable for public facing APIs since the secret must be shared with developers
- clients cannot dynamically build a GraphQL query at runtime using string interpolation, but I've never had a need for this and it is discouraged