As I am back in a Mac lab environment I plan on using Hype with my classes. Adding an animation to an iBook is made a lot easier with Hype 2.0. I 
took screen shots of the different scratch components I wanted and animated them. Then I took a screencast of the output in scratch and converted the video into an animated gif using GIFBrewry and added that to the animation as well.
Just a few steps:
create the animation in Hype 2
export the animation as a Dashboard/iBooks Author Widget
select the widget and drag it into your iBook
The software creates the default png from the opening scene of your animation. This is the widget in the iBook I am working on.