Lots in your post struck a chord with me as well.
One of my ds1's (10 next week, AS) biggest problems is over-reacting to benign actions/behaviour of other children. He tends to be convinced that they are always acting with malice of forethought and always wants them 'dealt with' by an appropriate adult (teacher, dinner lady, me etc). We have learned to take the tack of acknowledging and validating how he's feeling, but being firm with explaining that the other child has apologised and didn't mean it so we have to leave it in the past. It doesn't always work, but I think he has improved with it.
Firstly, I think a lot of our dcs are exhausted and have had enough by this stage of term - even my nt ds has been a proper old ratbag this past week. Ds1 suffers very badly with anxiety anyway, but the past couple of weeks he's been all over the place, tearful, angry, ranting, refusing to participate at school and his teacher has been shocked, because he is usually so keen to please his teachers and really polite and well mannered with adults in general. I think its come as a bit of a shock to her system after half an academic year of him being angelic for her, then coming home and taking out all his bottled up stress on us. 
Your ds could well just have had enough for one term and is overdue for his holiday.
The single biggest thing we've done to help ds was to get him to record his feelings using simple emoticons. Initially we just got him to give each day an emoticon at the end of the day and explain why he chose that emoticon, but now he fills in his feelings diary after morning play, lunch and just before he comes home. We have done a fair bit of work with him on identifying his own emotions and assigning them an appropriate word and number on a scale of 1-10. He identifies how he is feeling and assigns a word and number to it, then his teacher writes a brief sentence explaining what it relates to. So, say he's fallen over at playtime and is really upset, he might put 0, sad and then his teacher would write 'fell at playtime - cut knee'.
It has helped him develop an awareness of his own emotions and also to get them into perspective, as he will see that although he gave morning play a 0, he gave lunchtime and the afternoon an 8 and 10 respectively, so the day wasn't all bad. Prior to doing this he saw everything and every day as extremely negative and would describe each day as 'the worst ever'. We have just averaged out his scores for this academic year so far and he was amazed to see that the majority of his scores fell within the postive end of the scale. Presenting this information to him in the form of a graph really helped him to accept it as the truth - because obviously computers don't lie. 
On top of helping to develop his emotional literacy and awareness, just having five minutes of an adult's attention a few times a day and being able to discuss his worries or concerns with them, makes him feel listened to, understood, validated and more in control.
In addition to all this, he has a half hour session once a week with an inclusion teacher from ASD outreach, where all they do is discuss anything that has happened over the last week and come up with strategies for dealing with those situations in future. He has improved no-end since he started having these regular sessions, as again he feels he is listened to and validated by someone he has grown to trust. Perhaps this is something your SENCO might consider doing for your ds?
As for going somewhere away from the class to calm down, I think the teacher should consider this as an option - but needs to understand that if he is at the point of refusing to work - they have left it too late. He needs to go and find some peace before he reaches that point. It could be that the classroom environment is just too much for him for long periods and he needs to take regular breaks. My ds has a couple of 'jobs' to do that mean he can legitimately leave the room when it gets too much. (eg One is to keep the books on the shelf in the corridor tidy.) Other strategies she uses are getting him to take a note to the SENCO. The note is actually blank, but the SENCO knows that receiving a note via ds means he needs a break.