The plane will not go missing if the transponder fails. There are other means of communications as you might be aware of. This one is highly suspicious since it traveled additional milage..Or so we are told.
So is it possible that the transponder failed due to some reason ?? Then crew was busy in addressing that issue and in that process they failed to notice other emerging problems. May be just a simple case of poor resource management.
Then the question would be why didnt they communicate back ?