There's a lot of blame being thrown about after Hungary but if you want a pretty balanced view of the whole thing, the commentators from GrandPrix.com can usually be relied on to give an objective view of the situation. They wrote a sensibly impartial and analytical article below about Hungary which I suggest you read.....and then make up your mind
F1 - Grandprix.com > Features > Globetrotter > This whole business
McLaren has also stated that they a policy whereby each driver alternate on who will get the preferred strategy on each race. Hamilton got his at Nurburgring and at Hungary it was Alonso's turn. It happened in the first lap or two of Q3. Since burning fuel is all-important to a fast Q3 time, it is important to run as hard as possible for as long as possible. This means getting to the front of pit-out as soon as the car is capable of doing so, which means sitting there while the light is red, with the engine on, for up to 4 minutes. McLaren has stated that they send each car to pit-out before Q3 as soon as the car reaches a certain temperature. In this case Hamilton's car reached the temperature first.
McLaren has also stated that they have a strategy whereby they alternate which driver gets to be in front during Q3 (not who gets pole, just who is first on the track). The assumption is that this is irrespective of who manages to get their car to the front of pit-out first, since being at the front of pit-out is a competition between teams, and whether Hamilton or Alonso is the front McLaren during Q3 is a competition within McLaren.
There is a significant chance that the driver in front will get an extra lap of fuel credit in Q3, since it is possible he crosses the finish line slightly before the checkered flag while the driver in back crosses after the checkered. Since the 110% rule was abolished this year, and thus drivers can receive fuel credit for a qual lap completed in any time, this lets the driver in front run an additional slow lap that is credited and thus receive almost an entire lap's worth of fuel for the race that was not actually weight on the car in qual.
Alternating preferred strategies between drivers on alternate races probably meant that Alonso had never really been comfortable with this because it meant he did not have complete freedom to choose the optimum strategy for every race, but by and large he honored the understanding as part of the Team. You should therefore take this into account as it was Hamilton who openly admitted that he disobeyed this understanding and went against repeated team orders telling him to let Alonso pass during qualifying. It's likely that Alonso retaliated and the result was that he and McLaren got penalized.
Make up your own mind. Personally I don't believe Hamilton is the squeaky clean character that people think he is.