I think you have to learn to differentiate between Jobs and Apple. Apple NEVER owned Pixar, Jobs did.
Jobs was smart enough to realize that Pixar on its own was just a niche player, that might eventually get crushed by the big guys, but that it contained extremely valuable know-how to turn around an ailing giant like Disney.
Jobs was also smart enough that he has more pull as the largest shareholder of a giant company (Disney) than as a more or less ruler of a much smaller company (Pixar).
That Jobs' involvement with Pixar and now Disney also helped Jobs investment in Apple, that's a different story, but Pixar never was part of Apple.
How smart Job's moves were is clear from the fact that at this point he managed to get Apple in a position where they could just swallow Disney, and in the resulting share swap he might even become a controlling share holder of the combined company.