If you started rkt as a systemd service, you can stop the pod with systemctl stop.
If you started rkt interactively:
For a stage1 with systemd-nspawn, you can stop the pod by pressing ^] three times within 5 seconds.
If you're using systemd on the host, you can also use machinectl with the poweroff or terminate subcommand.
For a stage1 with kvm, you can stop the pod by pressing Ctrl+A and then x.