As mentioned, you need not sideload B&N content, even if you're sideloading other books. However, if you do decide to sideload B&N content (I run all books, B&N and otherwise, through Calibre's conversion in order to homogenize all books' appearances regarding paragraph breaks, smart quotes, etc.), all you have to do to get the B&N version to not appear is to archive it. This can be easily done through the "My Nook" area of bn.com, in the same place you can download your books. You can probably also do it through the Nook itself, but I've never tried so I can't say for sure.

This is something B&N gets absolutely right: it's very easy to get access to the ePub files themselves and it's very easy to get them off your device without actually deleting them from your account.