My headaches come from waiting for it to respond.
How close do you keep it when you're reading? I find that when I read my Sony, I have this nasty tendency to pull it close to my face. I need to consciously force myself to push the book away to a more normal reading position.
I found the solution is to buy the paper edition of the book I'm reading.
Addendum: just want to point out this is mostly just being cheeky. I enjoy putting down ebook readers for what they aren't, but I still use them for what they are.