Oh poor him. Your update makes it sound even worse.
The school sounds awful: the lack of respect for the issue, and the lack of care for your sons happiness, makes for sad reading.
Friendships is crucial. Absolutely key. My Ds1 has been very happy since joining secondary and I am truely grateful of his nice group of friends.
My other friend with a dd, has had very similar experience to you. One friend dumped her dd, then best friend left, her dd is so sad. Makes me sad.
My Ds1 On the other hand, is invited to tonnes and tonnes of parties (yes really!) , he's always out riding his bike with his mates, playing football with his mates, (rugby is a big thing at most of the local catholic schools aswell) , meeting at Nando's to have the Peri-Peri wings etc, - this is what your son should be enjoying!!
Please phone all the other schools. Again.
Are the local schools poor? All ours are very good. The catholic ones are excellent.
And finally, in the meantime, a polite, but undertoned strongly worded email to HoY, is needed me thinks!