Nate Silver arguably lost a good deal of "prediction calibration points" by placing a very low chance on Trump getting the nomination in the first place.
Not at all. A low probabilty does not make the prediction invalid because of the result.
And wouldn't the same be true if Trump wins the election? After all, Nate Silver isn't predicting a 0% chance for Trump to win, I think last time I checked it was 10-15%.