I have similar problems with using my macbook / iphone late at night in bed.
On the macbook, I use a nifty app called Brightness Control (freeware) that lets me set the screen *really* dim. Means I can watch movies without waking up my more saintly half. And longer battery. If I'm working on something in a window, another app called Think will black out everything except the active window.
On the iPhone, Stanza (free ebook app, and one of the best) lets me easily switch it to white type on black background, and a finger swipe on the text I'm reading can dim it right down to nearly black.
I expect Stanza on the iPad will do the same.