I'd like to politely disagree. I took the Hacking for Defense class at my school and had a completely different experience from the one you worry about. I think the most important misunderstanding to clear up is that the hacking in the class is not about hacking in the NSA/cybersecurity sense but rather the process of building something. Just like at a hackathon, students aren't all trying to hack the school's wifi etc., this class is about using a different approach to tackling military problems.

I've attached a link to our class website which contains a superset of the problems that my classmates and I tackled throughout the quarter. Hopefully you'll find it informative.

Class website: http://hacking4defense.stanford.edu/