Rory is just a nickname for Lorelai. Sometimes shortened versions of names don't always make sense... like Chuck from Charles, Hank from Henry, Peggy from Margaret, Libby from Elizabeth, Dick from Richard, etc etc. That's my assumption at least.
Again it's due to the confusion factor of having 2 lorelai's but I do think that you can get from Lorelai to Rory... here is my logic:
Lorelai can be shortened to Lora or Lor (like Chris uses in season 7) and Lor is like Ror and everyone always adds a y on the end of nicknames. Or maybe it is just backward logic as not much in the lives of Lorelai and Rory makes complete sence! Hope that you like my answer
Yes, I think this has crossed every fan's mind. I've thought of it as a chain reaction too. Take Lorelai, shorten it to Lorrie (the more traditional spelling), then for some reason substitute an "R" in there for the "L" and get "Rorrie" except spelled "Rory". That's my thought process at least.