The school show was abandoned after opening night when a razor prop wrapped in duct tape sliced the necks of two teenage actors. Both were rushed to hospital for treatment.
The incident is still subject to a health and safety inquiry by WorkSafe New Zealand.
The injured students have since returned to class.
A college spokeswoman said Mr Cole's departure was not related to the incident as he had been considering retirement plans for some time.
The board said there would be a new organisational structure put in place to manage the independent school's three campuses and four schools in Pakuranga and Remuera.
This would be led by a newly created role to lead all the schools supported by another new role of chief operating officer.
Over the past decade Saint Kentigern had seen growth at all of its campuses making the trust the largest independent church schools group in New Zealand.
It now had 2740 students and more than 400 academic and administration staff.
The board decided this was the right time to restructure given Mr Cole's planned retirement and the pending retirement of the trust's general manager.
Mr Cole will retire from teaching at the end of the second term next year