Renault and some other team were caught with the same offense and received no punishment, but that's another story.
I think the right move here is a fine in the millions and to disqualify Massa from the race. It's obvious to everyone what happened but Ferrari didn't actually tell Massa to let Alonso past. What did happen and what Massa admitted is that after some 30 laps of keeping his tm behind, he up and decided to concede his position and the lead of the race to Alonso. No mistake, nothing wrong with his car, just race manipulation.
It's really unfortunate, especially for Massa, but I can't think of any other reasonable way to punish Ferrari. Just way too blatant to let slide.