I think the fact that team orders were employed,whether openly or in this case a coded message saying "Fernando is faster than you. Can you confirm you understood that message?" is very clear,and was equally clear to the stewards.
What the FIA really should do now is to step on it pretty hard and send the right message.
For Alonso to say that both drivers had been doing their best for the team is of course nonsense,considering that he(Alonso) had been moaning that it was "ridiculous" that he was unable to pass Massa earlier.
The same result for the team would have been achieved with either driver 1st or 2nd,as long as a 1-2 finish was obtained.
Yes...we know it's difficult for F1 cars to pass at some circuits,and particularly in the dirty air close behind another car,but that's F1,and some teams seem to be able to let their drivers race,even if it does mean poor results sometimes.