I don't think it's so much that the Academy doesn't want a Kiwi to win so much as Jackson was a victim of numbers and other Academy politics.
The Academy wanted to nominate Spanish director Pedro Almodovar as a makeup for his film "Talk to Her" -- which received lots of critical acclaim as one of the year's best films -- not being nominated for best foreign language film.
Why was it not nominated? Because his home country submitted another movie for consideration instead. Each country is allowed to submit the name of only one foreign-language movie for considertation in the category. Spain wanted another movie to be nominated because Almodovar has already won an Oscar in this category, just two or three years ago.
So Almodovar was snubbed by his own country. So the Academy, which likes Almodovar and his movies, made it up to him by nominating him for best director and best screenplay. He won't win either category, but the Academy wanted to at least have him nominated for something.
To make room for Almodovar in the best director category, someone had to go. All the other nominees were directors of best picture nominees. Jackson was the only director who's film was nominated for best picture this year who was also nominated for best director last year. And everyone is basically saying the award is Jackson's to win next year once RotK is released, unless he botches the job terribly.
So the Academy decided Almodovar would be nominated rather than Jackson.
And you are right -- the Academy does want Scorsese to win this year, as a makeup for all the better films he made (Taxi Driver, Raging Bull, GoodFellas) in past years and never won the best director Oscar.