The next time the Kindle boots, it will discover the user FAT32 partition is corrupt (ntfs) and rebuild it.
Plus, the only (reliable) file system driver for writing to NTFS in Linux is a system add-on, which isn't provided in the system build.
So you will want to build that (and load it at start-up) for the Kindle:
http://www.tuxera.com/community/open-source-ntfs-3g/
Translation: Probably a waste of time, but I would recommend that you have a working serial port connection to the Kindle before you try it.