Tim Cook is more than ready to be "alpha dog". The amount of money that he is getting is specifically to keep him at Apple and not be poached by some other company. Steve Jobs has instilled the culture and I don't see much of a problem, they seem really good at getting rid of people (even if they spent time / money to recruit) if they don't work out.
Cook has done a series of corporate gigs (including ironically employment at IBM in 1984). But there's no history of entrepreneurship - no Apple, Next, or Pixar. He's Prime Minister not an Emperor material.
Churchill defended Britain, Napoleon conquered all Europe. Apple can survive with Cook at the helm, but nobody will describe him as visionary and creative (even if he is). With Jobs gone, the press won't be afraid ask, "Ping? What were they thinking?"