Without knowing the arrangements it is hard to say whether the 1:1 was right in not being there.
For instance do they cover meal times and breaks with your child? If so they are entitled to their own breaks during the day. This means for parts of some lessons your child may not have their regular 1:1 or may not have additional support at all during this time.
As your child does not have a statement the amount of support he is getting well above what is provided for and being paid for by the school. So yes the school has been very good with this.
There is a huge danger in supporting your childs 'logic' on this. Yes it does sound reasonable. It is this logic and reasonableness which could lead him to excluding himself from the curriculum and socially.
Would you for instance support this type of logic if the class went out in the afternoon and on the way back to school in time to be picked up he decides their path takes him nearer to where you live and decides it makes more sense to go straight home without telling anyone?
What ever the reasoning he removed himself from class without telling anyone. This was wrong. As a parent of a child with Aspergers I would fully support what happened.
As for what occurred in the classroom again without knowing the details I would not be quick to blame the 1:1 for this either. Again if the two boys rushed off they are in the wrong. However unless you wish to put your child in a harness or collar and have them on a lead there will be times when a child gets away from the 1:1. It may not even be necessary for the child to get away from the 1:1, things can happen very quickly.
Obviously I don't know what has been disclosed to his peers, though it may be worth considering if this has not already happened. I know this raises the possibility of bullying, but I do believe children are far more accepting then many adults when they understand what is happening.
If he does have autism then leaving him alone when he is upset is important. This can be easily explained to his class mates.
I do understand the SENCOs view point in waiting for diagnosis. The school is already going well above what is reasonably expected, and without a statement at their own expense. With the diagnosis the statement can be more centred on his needs.
This may sound awful, but to be truthful as I see it it was a minor incident, with a serious threat involved. With some autistic children it would have ended up with an assault on the other child. But it does put this into perspective. Unless your child is openly violent to others.
It does possibly leave some questions, ie when is he supported, the possibility of introducing a system where he can self time out and importantly if it is not sorted out yet where his 'safe' area is.
You say he has a new 1:1. I can recommend a good TA forum where they can ask questions and get to understand what is involved in supporting sn students with various needs.
Invariably schools will always concentrate on the consequences first. It is not always obvious what the root cause is. This is why it is important that we work in partnership with schools. I always seperate the two. Yes the consequences have to be dealt with first. Then I will discuss what the cause was and look at how to reduce possible occurences. Sadly the way most schools seem to operate if you try to tackle the two at the same time they think you are trying to dismiss the consequences.
I wish I could tell you it gets better. Last year I was told our daughters class had been told to wait outside the classroom. The teacher went off, came back and told them to follow her. Daughter did not hear her so stayed outside the classroom and watched the rest of the class walk off. In the end she went to the SEN department who went in search for the teacher. She had still not realised our daughter was not with them. This was the same form teacher she had had for three years. On that occassion as the school was aware of what had happened and had dealt with it I didn't kick up a fuss.