Great idea!
A couple of comments.
In the appendix, I would place notes/additional schematic on the two digital output functions about hooking up inductive loads such as motors or relays. Including diode protection to prevent frying chips.
You want to think about including advanced tabs in the booklet that talk about bit math, port manipulation, and maybe PWM with references to the data sheet and a couple of examples. Not sure about your audience but these may help introduce those students who are interested into a more general AVR programming with C. And it can prove useful to normal arduino activities when you need to change more than one pin at the same time.
Finally, I would include some web addresses in the appendix for where to find devices, arduino.cc, forum, etc...