I agree, Hamilton's race position is irrelevant. Hamilton didn't lose the race because of Vettel (other than the fact that the red flag probably caused this unfortunate eventuality).
The problem I think is that the stewards decided on a too lenient punishment (10s stop and go). In pretty much any sport, such an action would yield an immediate red-card / dsq on the spot. The fact that the stewards didn't is (due to not wanting to interfere with the WDC) what is causing the FIA to look into this. I also feel that the incident of last years Mexican GP and that Vettel is on "probation" for something similar to road rage is not quite irrelevant and may play into why he is being re-investigated.
As I said, I don't dislike Vettel, but IMO the punishment was not appropriately given. It should have been a black flag and DSQ right there. In that sense, the best outcome to this in my opinion would be a DSQ for that GP, but no impact on any future races. Confine the action to that race.
I also think that Vettel is silly for not accepting blame here post race. This may have been avoided if he had come out after the race and said; "Sorry, I misunderstood that to be a brake-test in the heat of the moment, I wanted to show him my annoyance but there was no intent to ram him. I'm ashamed that it happened bla bla ba" and my guess is this would have been far less of an issue than it has become.