I subscribed to the Stanford
CS193P: iPad and iPhone App Development (Fall 20011) course.
It looks like the videos are set up for streaming by default, but can be downloaded for offline viewing. Tapping on info icon on downloaded material give you a delete option. If this course is typical it should be possible to manage how much content is on the iPad directly from the app.
When you tap the gear icon at the top right there is an option to turn auto-download on/off. Off would seem wiser for courses with a lot of video and large files. Mine was off by default.
For iBooks purchased for the course you may have to delete them in the iBooks app. I'm not sure. There are no books in this course.
I'm still checking the video out. These are big, and will take a long time to download. It would probably be better to use the streaming option when you can.
Other courses may be different. Just have to experiment and see.
PS: I had to delete and re-download iTunes U before I got a subscribe button in the catalog. Irritating.
PPS: Looks like downloads can be canceled if you start them by accident. Just tap on the little progress circle/button at the right. Took me a couple tries before it stopped the download, instead of playing the video