I don't know the exact rule but I always thought it meant you couldn't overtake and keep the place, not that you can't go past the car in front by accident then let them retake the place again, in the BBC article Alonso even says he overtook Hamilton 2 or 3 times so if thats the case and the rule is you can't overtake at all then shouldn't he be being investigated to?
This is correct. In the interests of safety, if you can justify that you "overtook" or went ahead of the car in front of you (while the SC was on the track) for safety reasons, and the car/team that you overtook dont protest, then all will be generally fine. As long as you can explain your actions and relate them in some way to safety, its almost impossible for the FIA to reprimand that driver. Also, you must not gain a place by your action (The last point being very important).
IMO, Hamilton has nothing to worry about. He was very very close to the safety car (SC). It was seriously wet. In fact the conditions were so bad, that some drivers were pretty angry that the race even took place! While following the SC, Hamilton will argue that he got a little close to the SC and needed to brake and go wide, to avoid spinning and not cause a major accident and endager his own and other drivers' safety. Hence, he went wide. No one told Webber or Vettel that they had to drive so close to Hamilton. In fact, only an inexperienced driver would do something like that. Vettel - I can understand; but Webber - he really should know better.
When Alonso was behind Hamilton and the SC was about to pull off, Hamilton, in effect, brake tested Alonso, which is not sporting and endangered the safety of the following cars. However, consider that Alonso is in the same team and has a huge ego, whereby he is the best driver in F1 and if ANYONE CAN DEAL WITH HAMILTON, ITS ALONSO. It would make Alonso look like some sort of amateur if he went and complained. For those reasons, although Alonso could've complained, he didnt. In any case, he went off for reasons totally unrelated to any other car/team/driver.