I have zero problem with a hybrid setup. I'm not running Docker just for the sake of running Docker.
I'm running Docker (specifically Dokku) because it drastically simplifies deploying new builds, and graduating those builds between environments.
I know a large part of this article was that Docker complicates rather than simplifies the situation. I guess if you're trying to be a Docker purist (for no reason) then sure. The same is generally true if you try be a purist of any kind.