For example, a primary responsibility of HR is "keep the company from getting sued" when it comes to personnel matters. A really shitty HR department will interpret this as "sweep shit under the rug", but a good, competent HR department will handle things above board, according to established procedure. A good HR dept. does this not because they want to be nice, but they realize that the best long-term way to keep the company from being sued is to make sure complaints are handled above board.
In general, when evaluating how people will really act I think it's best to leave morality out of it, and instead realize where their incentives are coming from and try to align your goals with those incentives.
He said it himself in the article: When the general and his lieutenant disagree too much, the lieutenant must go. Sculley has made the right decision.
There can be only one CEO; if I'm not on board with the mission and direction that CEO wants to take the company, I don't belong there. As level-headed adults, it's time to negotiate the terms of my leaving...
HR represents your employer interests. Period.