Allaboutme, I was gobsmacked when I read your post. Ds1 (verbal dx of Aspgergers) gets really distressed at exactly the same scene on the TrapDoor DVD. Its the one where Boney leaves the castle isn't it? He gets really upset and we have to switch it off before the music starts. As you say, if the sound was off and he'd never heard it and made the connection with it being a sad event, I don't think it would bother him.
He's always been sensitive to music. When he was about 20 months old, we were shopping with him in the pushchair and a busker was playing some very atmospheric and emotional violin music in the town square. He sobbed and sobbed and all we could get out of him was 'sad music, no, no, no, sad music'. We had to get him away from there sharpish because he got so distressed.
He is now nearly 8 and although he has learned to understand that I am upset if he sees me crying and will come and try to comfort me, and he understands that babies cry because they need comfort (he has a 1 year old sister that he idolises) he can't generalise that to understand that all people that cry are upset or sad.
I think the music provokes the emotional response in them and it comes as a shock because, not being able to read the social and body language type cues of other people, they are not used to experiencing spontaneous empathic emotions. (Its difficult for them, but somehow I find it comforting, as it reminds me that the empathy is there in there iyswim.)