A work around is what I do. Essentially I organize everything on my PC, then copy & paste the whole kit and caboodle onto the SD card at once. The system saves everything, folders and all in alphabetical order.
Of course, there are limitations. This only works until you go to load another file or folder onto the SD card. the system will stick all new files/folders at the bottom of the directory. So to keep the alphabetical integrity, you need to delete everything on the SD card and copy & paste. A rather time-consuming activity when doing often and not very efficient. But honestly, I have so many roms on the SD card that I probably go through this exercise about once a year. So it's not so bad.