This is exactly the reason I use the Channel Locks feature to lock-out all SD equivalents to the HD channels. I have gone through the pain of setting timers for the SD channel when I THOUGHT I had made the timer for the HD channel. Tears. Got fed up and locked out channels. Also, my family will sometimes--while channel surfing--view the SD equivalent for HOURS not realizing that it is available in HD on the next map-downed channel. They can't keep track in their heads which channels are in HD (about 100 now). This happens even in Guide view because the list of channels shows the SD at the very bottom, so they tune to that not paging down once more to see the HD channel listed. This is the way the vast majority of people do this. They aren't techies like those on this board. They get a a bit upset at themselves--they are paying the extra $$ for HD--and a bit pissed at Dish for not having a feature like the Locals set-up where the SD's won't display.
Also, if you use the DISHPASS feature, it has among the options "HD Preference" and "HD Only." That is the one sure way I know it will only record the HD showing of a movie or any other show.