As the clerk is not involved in decision making then you could argue that they should remain in order to ensure that correct procedure is followed, that the decision is formally taken etc etc. However, the council could decide to ask the clerk to leave - they are the employer after all and the clerk must follow the instruction of the council. If I was clerking, I would offer to step outside as a matter of transparency and professionalism.
However, as you say, I cannot think of any legislation that requires the clerk to leave as legislation related to elected members rather than employees.