The rule was originally put in because fans don't understand the sport. If people are aware of the realities of the situation then team orders are natural and have been part of the sport for decades. If this had been 1950s F1 then Massa may even be called into the pit to give his car to Alonso.
There are similarities to the Tour de France. A domestique will surrender his bike to his team leader, or bust himself physically in order to help his leader get into position in the race. No one wails about Navarro killing himself in the mountains to help Contador, although it means Navarro then has no chance to win.
Massa is the domestique, Alonso is the leader.
Having said that, the rules are the rules and should be rigorously enforced, especially if the FIA considers that Ferrari have lied to the stewards, which would be much more serious than 39.1.