The thing was Massa was running faster, and realistically, Alonso would have not been able to pass him. Being told by his engineer to lap at a 3 second gap, and then suddenly Massa not only stopped running faster than Alonso but dropped well under the 3 second gap should have been a red flag to the race stewards. The reality was Massa was indeed pulling away until that order. The second order from his engineer telling him Alonso was now faster, that had no reply from Massa was the final evidence that Massa was being the good "second" drive that the red car team always seems to have.
Is Alonso ahead in the driver points, yes but not by much compared to Massa. And Alonso even with the points Massa gave him, didn't advance into contention in terms of driver standings. However had Massa won, he and Alonso would have been neck and neck in the standings. Given the fact Alonso has made a hash of Massa's races by knocking wheel rims repeatedly with his own team mate, the issue of whether Alonso is indeed the primary driver is questionable at best. There is no doubt Alonso is a great driver. There is little doubt that he will likely be a World Champion again. But by the same token Massa was 1 point away from being World Champion and arguably has enough talent to become one himself. He has been a good driver since his earliest days at Sauber Petronas, and his talent level is rumored to be one of the reasons why Shumi "retired", allowing the much younger Massa to remain at Ferrari as a driver.
I understand that they have almost always had a primary driver and a secondary driver. But with neither in true contention for the Driver's Championship, and the fact that the finish order would have zero impact on the teams Constructor's Championship standings, the thinly veiled race engineer orders should not have been ordered. I do however think that the ban on team orders should be dropped altogether. That way, in future races where this same type of situation exists, its public knowledge that a team is favoring one driver over another. Whether such favoritism is justified or not can then be fairly judged by the fans.
And as a full disclaimer I have been a McClaren fan since I was in the single digits, and loath Alonso for his prima donna acts at the team when he showed up trying to be the primary driver there. So I really hate both Ferrari and Alonso. Massa on the other hand I have always supported as a driver and I really hate to see him pushed back by Alonso.