I run some containers with the option --restart always.
It works good, so good, that I have now difficulties to stop these containers now :)
I tried :>
Just
sudo docker rm -f container
will kill the process if it is running and remove the container, in one step.
That said, I couldn't replicate the symptoms you described. If I run with --restart=always, docker stop will stop the process and it remains stopped.
--restart=always
docker stop
I am using Docker version 1.3.1.