Nice work, it is good to know this option is available if Kobo don't come up with a better way to store cover images by the time I reach the FAT limit.
I don't use Windows so haven't tried it, but according to Wikipedia
Ex2IFS will allow mounting a read/write ext2/3 filesystem in Windows.
Edit: Journaling support is not necessary anyway, FAT doesn't have a journal so you don't lose anything by formatting the card ext2 without a journal.