I've had a couple of experiences with friends or family in relation to school refusal.
1) Niece. At 15 became very resistent to school. Her mother sympathised and wouldn't force her. In the end, it was decided she could become home schooled, which in actual fact meant almost no work at all (I know this because I worked with her remotely, and she did almost none of the work I gave her). Her ambition was to be a primary teacher and she totally blew this due to not getting GCSEs, then A Levels, hence, couldn't go to uni. She's spent the last 10 years in low paid jobs and is still living in a bedsit.
2) A friend had a very similar situation with her DD to the OP. Daughter claimed to be ill A LOT. Friend was sympathetic and didn't force her daughter into school. At the end of the year, her attendance on her school report was four times higher than my DD, who had health issues.
I'm afraid, as a mother and as a teacher, I would have just forced both of these girls into school. I'd have every sympathy for how they felt, but wouldn't put their education on hold because of it.
As a teacher, I know schools can make lots of accommodations for students that are wary of school. There will be teaching assistants or a SENCO, or somewhere that can let them work outside of a classroom environment. At times students can be given work in the room of a teacher who is on a planning period (for supervision).
I also agree with Glorianny. There will be some sort of attendance officer or a head of year that can go out of school, to collect students. I do think that other than if a student locks themself into a bedroom, they should be made to go into school, unless a parent is prepared to take on active home schooling.
Life without a proper education isn't a viable proposition.