Their only mistake was making it so blatantly obvious. As others have said team orders have existed since F1 has existed. Does it make for the best thing to watch, of course not, but its part of the sport.
In the 50's, one driver gave up his CAR to his team mate because his own failed and he needed the points to win the championship. How would you guys react to this now?
The mistake was not even making it seem like Massa made a mistake or something that is not as obvious as pulling over on the straight. My feeling is the FIA will remove their points or do something else draconian.
And Alonso did try to overtake a few times once Massa came back out on the hard tires. Massa shut the door on him and Alonso would have had to divebomb him to get past, so for the sake of the team it makes more sense to have the driver with much more points win while keeping a 1-2 for maximum points. The teams want to win the constructors championship first, but the drivers championship is also important to them and that is the main reason for what happened today.