I also have this problem.
It seems to me that the wording of the question is unclear, as I don't think the issue is that the books are "uploaded" to the cloud.
In my case, I loaded an ebook on my laptop, and chose to sync it with my iCloud account. That made the book available on my phone and ipad.
In order to read the book, I had to click the little cloud icon in the top left corner of the book, which downloaded it to each device. However, after some indeterminate amount of time, the book will no longer be on the device and will have to be downloaded again.
The problem is that iBooks is deleting the local copy from the mobile devices, and what we need is a way to disable this behavior.