I Have a 1st gen iPad mini with the same issue. i deleted all the books I downloaded and they are all showing as being stored in the iCloud but the storage taken up by iBooks is 2.7gb out of a total of 16gb. I have asked Apple what to do as this has only happened since IOS9 which made iBooks a default app. They tell me I would have to re-set to factory settings. do you think the actions you took on you iPad will work on the mini?
i can't see any task bar other than the one running along the bottom of the screen which contains the mail, Safari, videos and music icons so cannot close the app from there