Create a automator application able to launch and quit from dock

Your app does start the process and then quits itself straight away leaving the process running.

You could try and check in the Automator action to see if the process is running. if it is quit it, if it is not launch it.

 isRunning=`ps aux | grep -i "Textedit.app"| grep -v grep`

    if [ $isRunning -eq "" ]; then 
        echo "is Not Running" 

/abspath/to/my-command
    else
        echo "is Running"  

# terminate code  here
    fi;

So when you click the App in the Dock. to will either start the process or stop it.

Opening an Automator application starts a process named Application Stub, but killall Application\ Stub doesn't terminate its child processes.

$ sleep 1 && open ~/Desktop/Untitled.app/ & sudo execsnoop
[1] 650
  UID    PID   PPID ARGS
  501    655    650 open
  501    656    143 Application Stub
  501    657    143 Automator Launch
  501    658    656 bash
  501    658    656 say

pkill -P $(pgrep Application\ Stub) and killall say made Automator show a dialog that the workflow encountered an error.

If you used an AppleScript application instead, it could be terminated from the Dock or with killall applet.

Or if you don't want to keep a shell window open, use disown or launchctl submit:

say {1..99} & disown $! # stop with killall say
launchctl submit -l my.say say {1..99} # stop with launchctl remove my.say