I don't think cheap supermarket shoes will cut it, commenters, if the boy needs special inserts and is recovering from a foot problem.
Sorry, OP. That really sucks.
Children take items of clothing off all the time outside at primary school: jumpers, hats, jackets, etc. And they also leave their waterbottles and lunchboxes outside frequently. That doesn't mean ANYONE should be chucking those items over a fence because they were taken off / put down.
That being said, a Reception child is just that: a REception child. 5 at the oldest. They'll know it's wrong, but they won't understand the extent of the problem for you.
The teachers and head, though, have behaved poorly: the teacher for initially refusing to believe it could have happened and then blaming the Y6 child when he had to accept that it did in fact happen. The head for also blaming the Y6 child. Again, children take things off outside all the time; often they are told to for a variety of reasons. The shoe should have been searched for immediately with the help of school staff.
I would be very cross with the school. I would also be making it clear that until my child's feet grew again, he would be wearing shoes he already owns, end of, unless the school is going to pay for a new pair.