I've been assured that the acquisition is much in line with how Disney works with Pixar. As in, Disney doesn't mess with Pixar at all, they just make money off of their awesomeness. And if that's the case, then fine. As long as this just means that Marvel movies have bigger budgets and wider reach, fine. I'm only worried about the universe getting even more splintered, with Paramount, Universal, Sony and Fox already in the Marvel sandbox. But then again, Disney probably has the money to buy back Iron Man, Hulk, Spider-Man and the X-Men if they so wish. Plus I have also heard that the current deal with Disney doesn't affect Iron Man 2, Thor, Captain America and Avengers. That's reassuring.
I'm also really excited about the animation prospects, as well as the possibility of Pixar doing ANYTHING with Marvel. That would be AWESOME.
As for the comics, Disney knows they know nothing about them and, again, I've heard from friends in Marvel that Disney won't mess with the comics. They know Marvel knows what they're doing and knows to not get in the way. If this does mean better kids comics at Marvel, or better marketing to children, and getting new readers into comics, then that is GREAT.
Also, Marvel stuff in Disney stores and at Disney World? That rules me.
I may be an optimist but I really don't think anything is going to change on the comic front, and I actually think that the movies will get even better. Fingers crossed.