Facing a similar situation a couple years ago, the solution I had pushed for was just for a few (3) dokku servers setup behind an nginx server as a reverse-proxy... the reason for multiple servers in our case was redundancy first, this split allowed us to do the exact same deploy to three servers, run tests, update nginx config then down the old version(s) of the apps.
Flynn and deis definitely seem interesting, as does the tooling that coreos and docker themselves are working on.
Flynn and deis definitely seem interesting, as does the tooling that coreos and docker themselves are working on.