That's what I thought until I found out that Pixar completely runs Disney's entire animation division now. Pixar's president Ed Catmull is now in charge of the Pixar and Disney animation studios (reporting only to Iger and Disney Studios head Cook), Pixar vice-pres Lasseter is the animation creative head, and several other executives moved over. Couple that with the fact that Jobs is now on the board and is the largest single holder of Disney shares, and Disney won't be able to easily beat-down Pixar. Also remember, Eisner, who ran Disney into the ground, is out.
This is almost like the reverse takeover Jobs pulled off when Apple bought Next.
Your analysis is exactly what I've come to think. Also, I've read that Lasseter and Roy Disney are great friends. Lasseter has also spoken out about the 3D (CGI) animation group that Disney was building after they closed down all of the 2D (cell) animation work in Florida and gutted the California team. Lasseter has said that he will assess that entire group, with some possibly being moved over to work with the Pixar folks, some being let go or some being assigned to a revamped 2D animation group. Lasseter is a big fan of traditional animation and wants to bring back that part of the Disney empire.
I even read one report that Lasseter is taking over creative duties for the parks, but that hasn't been confirmed anyplace official that I've seen yet.
All in all I think this is very good news.