A theory:
Maybe they did it because Apple has an unhealthy, top-down corporate culture that doesn't encourage dissent or whistle-blowing? Nobody said stop because it isn't the Apple way?
To me (not an Apple user or Apple employee) their corporate culture, their values, are defined by secrecy, leader-worship, and a particular kind arrogance. Not necessarily at the level of individual employees, but throughout the organisation as a whole. In such environments, especially when the company is highly successful and seems to be able to do no wrong, it becomes difficult for individuals and even groups to say stop. And even bad ideas and technologies gain momentum.
Apple is a great company, make great products, and deserve their success. I just hope that Tim Cook is trying to get rid of the leader worship that surrounded Steve Jobs.