To see what is taking up your iCloud storage space, from your iPad tap SETTINGS, then GENERAL, then USAGE.. then under the iCloud section tap, MANAGE STORAGE..
From there you can see how your storage is being used and delete data that you don't need taking up your space.
Why do you want to delete them in your purchase history? Those iBooks are yours and the history is like your receipt.
You used to be able to "hide" them by swiping the purchase in your purchased-list and selecting 'hide', but since iOS 6 (or, some recent update) the option to hide apps from your iPad or iPhone has been removed. You can still hide them in iTunes (Mac or PC) by clicking the 'x' that appears next to it in your Purchases section.
Settings -> iBooks -> Show All Purchases (set to no)
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