The odds are pretty good that any book you download from a store other than Apple's (such as Barnes & Noble, in this case) will not work in iBooks. This is because of Digital Rights Management (DRM) restrictions, not iOS 5 updates. With DRM, each major store "protects" their books so that they can only be read on that store's e-reader device or app.
The only suggestion in this case is to use an e-reader or app that Barnes & Noble supports. I think it's the Nook, right? But - with DRM, they'll never work in iBooks.
Welcome to e-books and publishers and DRM...