Should the doctor or the church decide?
I would guess for money issues.
Why would you say that? Rather it appears that the school board determined that narcolepsy in a teacher is a bad thing, and if they are going to pay someone for the job, they prefer a non-narcoleptic.
If it is a “called” position doesn’t the Holy Spirit decide when she should leave?
What makes you so sure He hasn't; a disability incompatible with the profession, from nowhere?
I believe I read that the Doctors said with her medication her condition was manageable and she could return to work. I also wonder what her "Call" covenant contract says. I would say that whatever the written contract says should be binding.