When I think of that quote, I usually think about it in regards to wanting to escape a big stupid company and form a startup, but that was not at all the context in which Jobs said it. He was telling this to the Mac team, which had become a kind of splinter group with its own identity within Apple. Of course, it's not just better to be a pirate yourself, sometimes the empire needs to hire some pirates. The navy can't be seen robbing Spanish ships after all (or devoting lots of money to zany projects like a graphical user interface on a personal computer).
I wonder if big dumb companies like Yahoo could actually use the pirate mentality/method to their benefit. Why doesn't Yahoo take a few million dollars in seed money and start a bunch of companies under its own umbrella using some of its own people? Give all the power to the engineers and the designers, skip the MBA-wielding drones that you've described above and let people that can actually make stuff set sail. Would it still fail? If any of the ideas did thrive, would the companies just be smothered when incorporated back into Yahoo? Would anyone even notice that a couple of million dollars went to creating several radical new projects?