If it's just about reading a file from usb and writing it to flash, you might want to have a look at filo. It should be easy to integrate the functionality of flash_rom into it, so you don't need a full blown
linux
system in flash.
That will be a good idea if FILO can launch the flash_rom program but I thought FILO is excepting a bootable image. So I guess the effort will be in "How to make FILO run an executable?" Don't' know if I miss anything.
gin