The school in Dalry in Dumfries and Galloway is projected to have just eight pupils by August.
The woman entered a sexual relationship with the 18-year-old after he had left school, a fitness to teach panel heard.
Drumduan School, near Forres in Moray, focused on more alternative, practical learning for 40 years.
Education leaders say some secondary schools are reducing timetables due to a lack of specialist teachers.
The school will replace the old Dumfries High School which was at the "end of life" more than five years ago.
The parents of a female pupil at the school had raised a judicial review over the council's policy on the matter.
A consultation on legislation and new national guidance will be launched by the end of June.
Dumfries and Galloway College wants past pupils, staff and the community to share their memories.
Scottish Borders Council will need to secure extra funding to build the new primary in Eyemouth.
