I accept that a functioning transponder may not have saved lives, either here or 9/11. We will never know for sure.
It would not have saved lives, that's obvious based on the fact that its an aircraft you are talking about.
Once the aircraft has been commandeered by miscreants, there is always going to be bugger all you can do about it until the aircraft reaches the ground in one form or another (i.e. whether they crash it or a government blows it out of the sky.... the result in terms of the lives of those on board is the same).
I suspect rather than creating stupid fire hazards by hiding away equipment, you will find the more obvious solution to MH370 is staring you in the face .... improved profiling and psychological monitoring of flightcrew.