That has always been the case in F1. Team orders have always been a part of the game. It doesn't give any team the right to break a rule, but when a rule is not enforced it should be removed.
Surely, as long as the rule still stands though, it should and must be obeyed? If not, why have rules in the first place?
There are various rules in this years formula 1 season. Some make sense, some don't. As an example: The rule about having to use two different tyre compounds. It's there and beyond for enhancing the "show" (which in turn makes the race more interesting, which in turn increases viewers and ultimately revenues which is why it's good for F1), there isn't much need for it. The same applies to the rule 39.1, which is for banning team-orders. It may not make sense to have it in light of it being a team sport, but it's there to serve a purpose.
If a team doesn't abide by it, it should be punished. Fair and simple.
I'm not arguing this because it's Ferrari, I'm arguing this because it's something that other teams so far have respected and Ferrari by not doing so, have gained a bit of an advantage. Even further, I'd go as far to say it's not the best sportsmanship behaviour and wasn't necessary, given both Massas and Alonsos position in the WDC standings and the stage we are at.
Alonso's behaviour over mic, nor Ferrari's outright criticism about staged and manipulated races doesn't really help their cause one bit.