I suppose another possible kludge would be to have a specific sketch which sole purpose is to write data (embedded in the sketch) onto the SD card. Then load up the actual sketch that's going to drive everything. But I hate having to go back and forth and ultimately that's not a good solution for the end-user (which won't always be me.)
Like I said, the SD card won't be easily accessible (it's inside of an enclosure), so taking it out to put in a card reader isn't an option without tearing open the enclosure each time.