I would have much rather seen the two Ferraris collide like the Red Bulls previously, but on the other hand I don't see how banning team orders makes any sense.
Running an F1 team costs more than some nations spend on defense annually. These are major operations that employ hundreds of people. Situations like this are common in F1, and it is only logical for a team to do exactly what Ferrari have done: position their cars for maximum benefit.
I'm no Alonso fan but I doubt he honestly would have wanted to win this way.