To be clear, I'm only working on integrating a binary data format, which is different from a binary protocol.

HTTP is baked pretty deep into CouchDB, which makes it hard to remove (but who knows, Couchbase seems to be having some success ripping it out). BigCouch (Cloudant’s distributed version of CouchDB) has the HTTP layer neatly separated through the Fabric library (https://github.com/cloudant/fabric), so it'd probably be easier to add a binary protocol there.