Yes, we added that feature for Couchbase Cloud. To add a database you PUT to its URL (/dbname) with a JSON body that's the same data you'd put in the config file's "databases" object. To remove a database you DELETE its URL; this doesn't actually do anything to the bucket on Couchbase Server, it just unhooks it from the Gateway.
The catch is that these operations don't update the config file. You're responsible for doing that yourself. (Or you can decide not to put the database config in the config file at all, and just issue a series of PUTs on startup.)
—Jens