The more I think about it, the more I tend to remember that the code itself for ADE/ePub is not too big, what is large is the working storage required to decode and display ePub.
I would see the easiest way for them to implement a hardware/firmware solution would be to modify the existing firmware to check for a card and see if there is code on the card, if there is then execute it, otherwise revert to being the reader it is today. On a card you can have the additional code and a reserved working space. When we would look at it it would just seem like one large file that was not a book/music/photo. Just a thought.