Executing beancount-fava to start it gives the expected message in the echo area:
Executing beancount-fava a second time, which is supposed to kill the process, simply restarts it:
Fava process killed
Fava process started
Ideally, executing it a second time would stop the server - and I think this is what you were going for based on the fact this message appears in the echo area (use view-echo-area-messages to see the log).