Apple - Ability to set even below the minimum brightness on iPad

Many people use the black on white mode to invert the color mapping for applications that will not specify more of the LCD to be grey or black and less of it white. Some blog articles call this "night mode" but it's a typical adjustment for people that have different visual abilities.

Settings App -> General –> Accessibility –> Triple-click Home -> “Toggle White on Black.”

Even though you can't reduce the illumination of the lights in the iPad further without a jailbreak, you can use this system setting to increase the amount of light that gets blocked in many cases by triple clicking the home button.

Also, many apps are being programmed to only draw in night mode where only red pixels are used. This also cuts down on the transmission of colors that our eyes use to constrict pupils and preserve night vision. This isn't a general solution, but for apps like Star Walk - this works very well in practice.

Depending on just how much you want the brightness lowered, you might consider applying a screen protector to the iPad. Reviews of the Splash Masque Screen Protector in particular mention that the display seems slightly darker when the protector is applied. The reviews take this as a negative, but if that's the effect you're looking for, you could exploit this side effect for your advantage.

In the absence of a non-jailbreak software solution, a hardware solution might be your best bet.

On a jailbroken iPad, you can use SBSettings to lower the brightness even further than the arbitrary lower limit that iOS normally allows.

Without jailbreaking, you can lower the brightness beyond the settings limit only in the iBooks app (as you mentioned), not system-wide.