Ahh, I understand the big file issues and saving on to SD card. SD cards are cheap, or free as I have a bunch of small ones from old camera's that would work perfectly.
Would a "reboot" stop the downloading if it's a big file?
Connecting to the PC to fix a download, or remove the file is okay also.
I would think most files downloaded would be either EPUB, MOBI or PDF, and you could grab some info off of that. If there's enough meta-data could you save it into folders like calibre? "/AUTHORNAME/BOOKFILENAME" ? Would make the directory browsing still useful.