I didn't try killing it from the command line. If I see something similar again (when I get my XO's back), I will try that to see how it goes. I wonder, for instance, if Sugar would recognize that the process has been killed and remove the icon?
In any case, this message was less about my specific problem, and more about something which I think is needed. I'm not against people going to the command line, but I don't think they should be required to do so in order to make Sugar and Sugar activities work.