There are a number of options.
Firstly the school are not being as supportive as they should, he would be better registering at a 'medical PRU', now this isn't a PRU for the naughty kids, it's one for children with medical needs.
You should contact your local authority for information.
OK now I have said that, I realis it isn't much use now. But there are still options.
The most obvious is to have him resit the year, you have to ask the school about that.
Does his school have a VI form?
Another option is home tuition, which probably won't be full time.
If he leaves school with no qualifications then he can go to an FE college and start with a level 1 qualification (this is pre GCSE level) followed by a level 2 and then level 3 (A levels or equivalent) he will also sit GCSE maths and English.
A final option would be to do correspondence course GCSEs at home with him sitting the GCSEs at school.
Obviously you both need to talk about how realistically he can achieve qualifications whilst still recovering.
On the limited information you have given if his school has a VI form him going to VI form, but sitting a reduced number of GCSEs. This way he would be with friends for social interaction / support but taking GCSE classes with year 10/11 with the aim of getting 5 good grades.