We have been running Docker in production for around six months now, with a moderate IO load. We are also using persistent storage, but our persistent storage is NFS-mounted inside the container, so 99.5% of the filesystem IO in the container does not touch AUFS. (We are stuck on an old kernel at the moment, but evaluating upgrading to either 3.x or 4.x.)

So far, this has been stable for us, and based on your post it sounds like it will continue to be a viable strategy as we move to kernel 3.x or 4.x.