In fact, I found the answer on a French Forum. There is it :
Connect to the Store via iTunes for Mac (I think it works the same on windows but I didn't test)
Choose "Books" on the up "headband" (I don't know the English word, please correct :) )
Click on purchase on the right column
When you mouse over the book you want to delete, a X will appear. Click on it and your book will be hidden. It will be possible to download it again (for free I think, but again I didn't try) but it won't appear anymore in any of your device.
Et voilà ! I don't have this book on my iBook library any longer!