No matter how good you are as a manager in as much as you were hired by a person or group of persons, you are answerable to them because there are conditions and reasons that made them to hire you as such you don't act on your own, although many managers has used their coaching strategy to bring success to a club and thats the purpose for their employment but before you make any step as a manager, you must involve the owners of the club before anything although sometimes club owners are very annoying in terms of decision making.
As for morinho we know that he is not a bad manager but he is arrogant although am not judging him because different people has their personal character but I believe that what happened may be as a result of his attitude and nothing else.
Mourinho or anyone else, if you are a jerk to owners or the other office management team, then you are going to end up with trouble. Directors are there for a reason, and if you are a jerk to them then you are going to end up with a bad result. Mourinho realized too late in his life (probably right about now) that he needs to listen to the owners and presidents of clubs to keep his job, even a cup may not protect his job, he has to do better.