I had eye-strain problems while reading books on my iPad at first, too, even using the Kindle App. I solved the problem by slightly increasing the size of the font.
Now my main complaint is that the iBook application uses up the battery too fast. I can switch the Kindle App text to white on black, but that option does not exist in iBook.
Not in the iBooks app, but you can go to Settings -> General -> Accessibility and reverse the colors on the screen across the board. You can also set it so that a triple-click of the home button reverses the colors. At least that's how it works on the iPhone; I haven't tested it on an iPad.