If I recall correctly cars 2 was made by Disney and then marketed as a Pixar film.
You're remembering incorrectly. Maybe you're thinking of Toy Story 2, which started out as a direct-to-video sequel that Disney commissioned, because they had the rights to do so. Pixar was concerned it wouldn't be very good, so they agreed to take over the production of it and made it into a full movie and it was released as a Pixar film.
But that kind of thing had stopped by the time Cars 2 was produced. Disney had bought Pixar, and essentially cleaned out their own animation studio's management and put Pixar people in charge of everything, because it was obvious to them which group was making better movies at the time.* So while they technically still maintained two separate studios, at that time it was really Pixar taking the lead over Walt Disney Animation instead of the other way around.
In any event, Cars 2 was a brainchild of Mr. Pixar himself, John Lasseter. It was produced from the beginning as a Pixar film and directed by Lasseter.
*In 1999 Walt Disney Animation released Tarzan and Fantasia 2000. Pixar released Toy Story 2. Pixar released Monsters, Inc. the year Disney Animation released Atlantis: the Lost Empire.
Pixar released Finding Nemo between the Disney blockbusters Treasure Planet and Brother Bear. The Incredibles, hardly Pixar's strongest entry, was still miles better than Disney's 2004 movie Home on the Range.
It's not real often you see one company buy another and then replace their own people with the other company's instead of the other way around, but man was it warranted in this case.