What you say is inherently true but highly unlikely. Firstly Aquarium pumps are by their very design extremely reliable items, (if you are using a quality type like an Eheim). Secondly Windows by design does like to lock up when shutting down occasionally, however I'd put money on the Pump being the more reliable of the two, The odds of both crapping out together must be extremely high, I'll take that chance.
The point is I have my protection up and running, it's working at this moment, and would power down my PC now if the pump failed or flow stopped. Some of the ideas posted here are brilliant, but ideas wont power down the PC, and maybe we are bordering the line of dismissed returns with all this.
If someone can show me a proven cheaper simple way that is as reliable or more so, I'll congratulate them and use myself, until then I'm happy to trust my windows app based system in the very unlikely event the pump should die, because it's far better than nothing at all , I test it at least twice a week by stopping the flow. So far it's never failed to shut off the system in the proper way within 20 seconds