In my uninformed opinion the issue goes as follows:
SE builds a platform on which a community develops with a fair degree of independence.
SE decides that a community representative is no longer to their taste, and they summarily dismiss her
A mild uproar ensues
CTO writes I am sorry to placate the uproar
and we are back to square one, with nearly no change.
They wanted to show that they are the sole rulers of these lands and they have done so very clearly. The next time they decide that someone else, or some other topic, or some content, is not to their liking, they still retain the same power and most-likely the same mindset to do as they please. Maybe they will be more subtle, if the negative publicity was ever amongst their concerns, or less subtle if they will think that any publicity, positive or negative, is still publicity.
To my understanding there is no plan to separate the powers of SE the company from SE the community. There is no plan to prevent future abuses. There is no plan to give the community the power to undo these abuses.
We are millions, that is true, but together we do not hold one millionth of the executive power of the last of SE's staff who lurks around these forums with a watchful eye. That is why the issue still stands.