What was frustrating with the Alonso/Hamilton/McLaren times was that McLaren made large gains thanks to Alonso's development skills. Hamilton benefited from those developments. Towards the end of the season, Alonso was pretty much ousted from the team. One of the main disadvantages he had to face was not being allowed to race under his preferred type of brakes. He was just told to "come race", and with all that, I still think he preformed brilliantly.
Well once he and De La Rosa went to the FIA and said "Oh, by the way, yeah, we really did use the Ferrari team data and management lied to you" he pretty much slit his own throat at that point. Especially since he didn't do it to be "noble", but to knife McLaren in the back.
McLaren is very much a "team" environment and if Alonso thought he was going to be Alpha Dog and get everything handed to him, he should have just watched the Prost-Senna years at McLaren.
And I was under the impression that McLaren was willing to run different brake manufacturers for each car when they could. Some circuits just demand a certain spec (be it Hitco, Carbon Industries, or whathaveyou). I could be wrong and might be thinking of other teams or the current season, but the SPEED TV guys usually note what brake manufacturer is on what car and point out if two cars in one team have different brakes.