100%this is what will happen.
Mistakes were made but neither team are at fault - ergo - thing stand as they are... Masi gets booted.
I don't understand this argument. It doesn't matter if neither team were at fault.
Its like the argument some people seem to be making that they can't take it from Max because that would be punishing him for something he didn't do.
It would indeed... much like not giving it to Hamilton would be punishing him for something he didn't do.
The fairest thing to do is to decide what "should have happened" and what the outcome would have been. That means Hamilton would take the race win and the championship.
They won't do that though and like you have said, Masi will resign and the result will stand as is.