I think he had to go.
My guess is that Liberty/ FIA wanted to see a titanic struggle that went down to the wire, with drama and excitement until the final metre. Fantastic for the fans, the sport, the sponsors, the marketability and the business. But, instead of just hoping it would happen, they tried to make it happen and they ended up with a huge own goal. The season climax was suddenly an embarrassment that had tainted the sport, and everybody knew it (Liberty, FIA, F1, teams, drivers, sponsors).
Board rooms would have been full of "This is a disaster, and it must never happen again"
They needed new processes to ensure that future WDCs are not tainted by suspicion or speculation. Out came the whiteboards and the workshops until...
"Perfect! Well done, everyone. That will work. Ok, so we have our new model that's not tainted. We just need to put some names in there. Michael as Race Director? Hmmm, hang on..."
He's too tainted to stay in that role. He really had to go.
Is it harsh on him? Perhaps. He was clearly under pressure from Merc & Red Bull, but I expect his own bosses were trying to influence him too. He was left exposed.
Is he a scapegoat? Probably, if he's the only one who lost his job from this. I imagine that if we knew all the circumstances, we'd be saying that a whole bunch of heads should have rolled.