Managing giant eBook collection with iPad after iTunes update broke compatibility with Calibre?
I had the same issue when iBooks got updated. The way I access Calibre when on my iPad is to put my Calibre library in Dropbox. Then, I can just access ebooks in Dropbox and 'Open With…' iBooks, read them, and delete them again. I used to do the same thing but using the CrashPlan app; either would work (it basically depends on what cloud storage system you have the most space with).

It's inelegant, but there's no more elegant way that I can think of.