Well, I can totally understand this being a problem for our little ones. Having a change to the routine is enough to get them a little frustrated by itself, but then dealing with a teacher all day who doesn't know him or know how to handle him or how to relate to him could DEFINITELY be enough to set him over the edge.
I know that this is WISHFUL THINKING, but maybe you could ask the school to contact you in advance in the future if there is going to be a sub. This way you would have time to prepare your son before he goes into that situation. I know they will ALWAYS handle things better, even difficult situations, if they are aware of them in advance. Now, I know that sometimes in emergencies, there may not be time to notify you, but for instances where there IS time, they should consent to this. Again, maybe this is WISHFUL THINKING, but I think our school would do something like this if it were going to help.
If I think back, WAY back in the day....I seem to remember there was ALWAYS one or two teachers who NEVER had a sub because they were like NEVER GONE....and for most kids, that's boring because sub days are supposed to be exciting, but for our difficult child's maybe it would benefit to try to find the teacher who is "never gone" or "rarely gone" so that the situation might not come up as often.