The issue in brief:
1. Passing the safety car is not allowed
2. Lewis Hamilton passed the pace car
3. He was penalized and force to do a drive through the pit lane.
4. That is the standard penalty
Everything else is just noise. Mostly from Ferrari and Alonso. Essentially Hamilton passed the pace car when it was mighty close to coming on track and I think he knew when he committed to passing that he shouldn't have but it was too late. Because he made it past the pace car he was able to finish second and Alonso finished 11th, out of the points. Alonso is mighty pissed because it means that Hamilton is well on his way to another championship pulling away from the Spaniard.
Alonso's claim that he "always plays by the rules" however, is hilarious.
In Hungary in 2007 he stayed in the pit allegedly "discussing tires" or something while Hamilton sat behind him unable to refuel for further qualifying. Alonso knew that he currently had the lead for pole and that Hamilton was surely going to outqualify him so he screwed his teammate. Oh, did I not mention that? He was willing to screw his sponsors, and his team (out of constructor's points) in order to serve his own interests. Asshole.
In Singapore in 2008 his team principal Flavio Briatore order the junior team member to crash at the worst possible spot on the track to ensure Alonso had a safety car until the end of the race ensuring a win. Not cheating there either? (NB: the junior driver later confessed to tanking the race on purpose which resulted in a force retirement for Briatore)
Ferrari is known by fans as the dodgiest team on the sport. In fact, they have a slang term called "red horse rules". It's shorthand for "the rules don't seem to apply to Ferrari (again)." This is especially bad when Ferrari is racing at home (Imola and Monza).
Frankly the fact that the whole thing meant that Hamilton didn't lose a spot and Alonso ended up out of the points makes me smile. Frankly, the both got what they deserved.