If you tap on the screen, does it display/toggle a set of controls? I do not have a audiobook but on a playing podcast there is a back button in the lower left hand corner that gets me back the home screen that has the Library navigation sidebar.
Unfortunately, I think that is the design of the iPod app - to mimic the behavior of the iPod device. Usually with a computer program there is a way to fully quit the program and on startup it starts from scratch. The iPod app design seems to assume you always want to quickly return to the last thing you where doing with the device. Even if you kill the iPod app, it will try to pick up with the last thing it was doing when you restart it. Even though the iPad hardware is more capable, the underlying architecture is very limited. The iPad is not going to be able to run to far ahead of the iPhone and iPod devices. I think to some extent, the Apple apps serve as basic and/or demo apps. Once you get use to them, it may be worth looking at other 3rd party apps that provide similar functionality.
I've learned to block out the Now Playing section of the iTunes/iPod interface because I can never get the correct covers to appear. Hopefully Apple will improve the iPad version of the iPod app's design over time. Right now it is pretty clunky and wasteful.
Thanks for participating on the boards.