If you want to do this I would suggest trashing MS OneNote, since MS
is very short sited these days, and go to a product that does which
is Treepad.
I use treepad for my knowledge base, project management, Motorcycle
trip information, etc and it runs on U3 usb drive and your pc.
http://www.treepad.com/
You are right if MS would allow this software to be on a U3 drive,
which they could if they wanted to but you know $$$$$, that would be
a great thing and sell more of their product.
Anyway just a suggestion take a look at treepad and see what you think