Sending a message only stops the clock on Response Rate. For a Reservation request, you must create an "action" - decline or accept. If they only sent an inquiry, messaging is fine and still counts toward your Response Rate.
I understand that you don't think it's fair. You can try to plead your case with Airbnb but it's your responsibility to host to the standards Airbnb has required. The fact that the guest made the error, is, indeed, problematic. As hosts, we are held to a higher standard of understanding of how Airbnb works. There have been plenty of times I've counseled a guest that I have only 24 hours to make a determination and if they do not respond, I will be forced to decline and they will not be able to book with us. Perhaps this techinque will work for you on the next opportunity.
https://www.airbnb.ca/help/article/363/what-does-each-reservation-status-mean
https://www.airbnb.ca/help/article/430/what-is-response-rate-and-how-is-it-calculated