I have just found this thread. I haven't read all of it, I haven't got a child with special needs but this is my experience of having a child with SN is class with DS1 in Y1 & Y2
DS1 goes to quite a large primary school, most year groups have 2-3 classes.
In Y1 he was put into a class with R (Autistic child). DS1 was put onto the top table with R. I didn't know R had SN, but when talking to DS1 about school he often mentioned R, how clever he was, how he'd completed X,Y and Z on a computer game etc
After school one day, a friend of mine asked how DS1 was because R had had a huge meltdown in class, throwing things and kicking the TA. I was
I later asked DS1 about this and he said. " don't worry mummy, R has Autism, sometimes he gets upset and does things, but (teacher)&(TA) know what to do and then everything's fine."
I talked to the TA and she told me how fantastic all of the top table were with R. That R was very settled within the environment and they were all very supportive.
In Y3, R was moved into a different class, despite his TAs wishes to stay with the class he had been in. His behaviour deteriorated, as predicted and now he has moved to a different school 
So I suppose what I'm trying to say is, to the OP, maybe the disruption is due to settling in issues, perhaps given time things will settle.
To parents/carers of SN children. My DS accepted R as just another child. He was impressed by his intelligence and computer skills. He knew the reasons why he was disruptive, because it was explained to him (as part of the class)
I believe he gained some great life skills, acceptance, working despite disruption and also I think it gave him a push to do better academically. 