At any rate, you bring up two points: First, that etcd is insecure, which is a problem in itself that needs to be addressed. Communications between K8S and etcd and between applications and etcd need to be secured, and K8S itself needs role-based ACLs in the core.
Second, for the Vault use case, the best practice is not to place Vault tokens in etcd that grant direct access to any secrets. Instead, the best practice (as Kelsey's vault-controller project does) is to pass a "wrapper token," which is a single-use token. The application consumes the wrapper token (hopefully quickly) and exchanges it for a longer-lived token, which can then be used to access the secret data.
Once the wrapper token has been used, it is subsequently worthless to someone who has direct etcd access. And Vault's auditing capabilities can help you detect misuses of wrapper tokens.