Wouldn't it be better/safer to deactivate the TOWS - exactly like the aviation relevant systems - by activating a relay?! Better a warning signal too much than missing one.
Your question is very valid. But I'm not so sure I agree with "Better a warning signal too much than missing one". I believe many studies have shown that too many false alarms affect the attitude of the crew so that real alarms might not get the attention they deserve.
And at least in this particular TOWS circuit, your proposed relay logic would in case of relay failure [unless the TOWS includes some additional smart logic that I have missed] trigger an alarm that would sound during the whole flight as long as flaps are retracted. Does not sound like a viable solution. It would need some additional logic to enable the crew to inhibit that alarm, introducing additional potential points of failure in the TOWS system.
Today's computer systems give a totally different capability to design an idiot-proof air/ground sensing system. But the MD-80 was certified in 1980 when microprocessors were in their infancy.