Another option would be to make a minimal install and then just clone the SD card. It's less neat than Docker, but if you're provisioning a new Pi then you still need to install Docker on it in the first place. Or use something like Ansible to do the setup automatically?

Hardware control on the Pi is pretty simple, use the WiringPi library. I guess you'd need to run Docker in privileged mode, but it should work from within a container?