The SD boxes do not have the ability to "receive" (not the best technical word, but used for better understanding) any of the HD channels, so Dish still has to send out the LIL's in both SD and HD. However, both Dish and Direct are working towards what you said in your post: only having to send up one HD stream of that channel so that everyone can receive it and SD subs boxes can down-convert it to SD, but that would require a complete swap-out of legacy boxes with all new ViP boxes. That would be really expensive. That isn't going to happen soon, but it is their goal for the long-term future.
However, Dish will be soon swapping out legacy SD QPSK boxes for more recent models capable of 8PSK for SD. This will allow Dish to put more SD channels per transponder (with about the same picture quality). This will free up transponders for, presumably, more HD without having to acquire more satellite slots.
Also, Dish has something called the Eastern Arc that was implemented last year. All new subs in the eastern portion of the country (with a few exceptions) must look at a separate group of satellites where all the channels, both SD and HD is in MPEG4 8PSK. Those subscribers must also have ViP boxes only, as those are the only ones today that can handle and display MPEG4 8PSK. So, the Eastern Arc is actually the more efficient system you suggested in your original post
Your suggestion is right on, but, as with any business, no matter how great the new technology and better the solution, we always have to contend with LEGACY. Hope that made sense.