One of my children boards - he has just started his second year.
I would say that, like with any school, some just aren't the right set up for the individual child. This is something I bear in mind all the time with all schools..having a terrible time at any school can be damaging even if it is a local state primary, day school, etc
Having said that the emotional impact of boarding has been hard for us as a family. My son loves his school and has made lots of friends etc.. He says he doesn't get homesick at all - so happy and busy we never get calls from him - however we have had a couple of meltdowns after the long summer holiday and Christmas holiday.
He says that it's hard to leave home but when he is there he is fine. We did explore all options but ultimately every one of them is a compromise and has an element of pain attached with it - om balance is whatever pain you can love with as a family.
My advice would be to pick your son up for a weekend to understand why he is feeling that way. You need to work out whether it just him coming to grips with change or whether he hates the school/ is getting bullied.
As an example, in his previous school my son used to cry and complain most days after school with tales of incidents and I lose count of howany time I had to step in... At his new school there has been none.
For what its worth I would not follow the school advice but I would see my son face to face to understand the situation better. If he is being bullied or has other issues, he will feel terrible. Let us know how you get on, I know it's hard.