Why is Tim Cook doing stuff Steve Jobs would have never agreed to?

Because he is Tim Cook.

Before he died, Steve Jobs told Tim Cook “Don’t try to be like me. Be like Tim Cook.” (Or words to that effect — I don’t have the source in front of me right now.)

Tim Cook is a different person and he sees the world differently than Steve Jobs. He manages Apple the only way he knows how — like Tim Cook. This is overall a good thing. Under Tim Cook’s leadership Apple has taken steps to improve worker conditions in factories overseas. They have made far more charitable donations. And, for better or worse, Apple has actually taken a stand on several issues — something Steve Jobs never did.

Look — Steve Jobs is dead. I don’t hear you asking why the CEO of Ford Motors is doing stuff Henry Ford would never do, or why Barack Obama is doing stuff [insert name of president here] would never do. Leaders lead according to their own style. Tim Cook is leading Apple as only Tim Cook can.

EDIT: I do not mean to infer that Steve Jobs did not take a stand on anything. Of course he did. But the things on which he took a stand almost always had to do with technology and Apple’s relationship with it. He did not feel it was Apple’s place to take a stand on some of the social, political, and charitable things on which Tim Cook does, which is what I mean is the difference between the two.