I am quite sure I read back then, that Alonso and Hamilton alternated between starting Q3 first in 2007. I believe that this was said during all the discussions about Alonso's penalty after qualifying in Hungary. I would like to emphasize the following statement from the race stewards:
At the commencement of the third period of the Qualifying practice it had been agreed within the Vodafone McLaren Mercedes Team ("The Team") that Fernando Alonso would leave the pit exit ahead of Lewis Hamilton in order to benefit from the possibility for purposes of fuel burn allowance of being able to complete an additional lap.
http://www.autosport.com/news/report.php/id/61373
Hamilton ignored this agreement and went in front of Alonso, and he also ignored repeated requests over the team radio to let Alonso pass. The reason why I mention this is that Hamilton had been faster than Alonso in Q2 (and he was also leading the championship at the time), but he still was asked by the team to yield position to Alonso. Hamilton did a lap of 1:19.301, while Alonso did 1:19:661. So the claims that McLaren decided who should run first in Q3 based on Q2 times do not seem to be correct.
I don't know if the Q2 times is a good measure of the driver's performance back in 2007. I would actually think that the Q3 times gives a better idea, especially under normal circumstances when we could see how much fuel they had been carrying based on when they made their first stop. Q2 was usually no concern for the McLaren (and Ferrari) in 2007, as they usually had a margin of at least 1 second to the 11th fastest driver. I am sure there would be some correlation, as an excellent driver would still be faster than a mediocre driver. But I think this correlation would be greater in Q3 than in Q2, so I don't really see the point of looking at the Q2 times.
