Intruder :
I am not familiar with the term " wetware" , but I guess you mean : "humanware " correct ?
Mixing highly complex automated system with humans reactions has always been a good recipe for disasters, not only in aviation.
You said :
If Pilots follow TCAS RAs instead of contravening ATC instructions,[...] there would be no requirement for the software change.
Absolutely agreed . But the fact is pilots do not always follow the RAs in that case as many large scale data collection studies show, and post 2002 incidents investigations still show.
So many solutions : I give you the main 4 : 1 : change/retrain the current pilots and/or replace them by kids that will not challenge computer generated advices, 2 : link ACAS to the auto pilot, 3 : modify the software, 4. Accept a certain non compliance percentage and the accidents/loss of lives that will result because of that non-compliance.
Incidentally , for the anecdote , Airbus, just after the 5 A320 landing accidents following its introduction , proposed a mixture of solutions 1 and 3 .