Isolating databases behind APIs and rev-ing API+schema separately is not enough. When the schema changes, data must be transformed to match the new schema version. As you point out this takes too long with a large database, and it doesn't account for data consistency.

We have been working on building what we hope are the procedures for this with ChronicDB (http://chronincdb.com). But it turned out harder than it seems, and we are not sure it will quite work out. We'd welcome feedback.