Magnaminous. Not a trait applied to second place very often, but in this case, like last time, a slowdown-lap radio transmission summarised the key point of a race better than a hundred commentators could (though Eddie Jordan, bless him, did a very good job of trying).
To address the point of whether, from the point of view of the race in isolation, it made sense for Felipe to let Alonso by, I offer the following graph:
Firstly, I apologise for the graph's small size. If you want to see it full-sized, please download to your computer and zoom it in.
Secondly, an explanation of the graph. It shows who had the largest number of faster laps of the two Ferrari drivers up to each point in the race. If the graph goes upwards at a particular point, then Massa was quicker than Alonso on the previous lap. If it goes downwards, Alonso was faster than Massa.
Note that the graph does not take the extent to which a given driver may be faster or slower into account, only the bare fact of who beat who.
For the first 14 laps, Massa is generally quicker than Alonso, but Alonso occasionally does one better than his team-mate. Towards the end of that 14 laps, "occasionally" became more frequent.
From lap 15 to 22, Fernando and Felipe traded faster laps.
Laps 23 to 27 see Felipe get an unbroken run of faster laps, cumulating in his strongest intra-team position of the race. By lap 27, he'd had 9 more "faster" laps than his team-mate, indicating that he'd been faster for two-thirds of the race up to that point.
Laps 28 to 38 are like an inverse of the first part of the race: Alonso has the upper hand for most of the time but Massa sometimes gets his own back.
Laps 39 to 45 see a second wind from Felipe; for all but two of those laps he is quicker than Fernando.
But after that the wind seems to have gone out of his sails: Fernando records all but 5 of the "faster" laps for the 21 laps remaining of the race.
The message, "Felipe. Is. Faster Than. You." came over on lap 48. At that point Alonso had been quicker for the previous 2 laps, so on a zoomed-in viewpoint, Fernando would have had cause to believe himself faster. Especially since he'd just hit the dirty air of Felipe's car.
However, take the last 10 laps, say, and it's quite another matter. Then, it's evens as to which of the two was quicker. The further the situation is zoomed out, the worse it looks. Especially since Alonso's gains mostly came in two discrete blocks (hence why Massa had still been faster for 3 more laps than Alonso at the time of the radio call). One of those blocks was when Massa made a series of mistakes getting used to new hard rubber and the other mostly happened after the team-breaking order.
In normal conditions that race, Felipe was faster.
It's not even as if Ferrari need to put all their firepower with one candidate yet. The gap between their drivers was less than for 2 second places, which given the team reliability and operational skill so far is easily made up in the 9 races that remained at that point. The gap to the leaders was wider, but either driver could still have bridged the gap. It was far from mathematically impossible for either.
Therefore, Ferrari have managed to incur the wrath of the FIA and its supporters, as well as damage its intra-team relations, for... ...not an awful lot of justification.