Julia Robinson had been the school's head teacher for two years
A Sheffield head teacher who wanted to scrap separate assemblies for Muslim pupils has resigned from her post.
Julia Robinson, who the local council claim resigned for personal reasons, faced complaints over her plan to hold one assembly for pupils of all faiths.
Her replacement said Meersbrook Bank Primary School did now hold one "daily act of worship".
Mrs Robinson called for a "constructive debate" on the issue and said she had wanted an "inclusive" environment.
Council leader Paul Scriven explained that the school had acted with the "best interests of all its pupils in mind".
He told BBC News: "The head teacher has not been forced to step down.
"The head teacher resigned for personal issues and she's made it very clear it's not related to this particular incident."
Sonia Sharp, Executive Director of Children and Young People's Services for Sheffield City Council, said: "Mrs Robinson was a highly regarded and professional head teacher who always acted in the best interests of the children and the local community.
"Her resignation was reluctantly accepted due to personal reasons.
"She endeavoured to make sure that every pupil in the school worked together to benefit from a happy learning environment.
"Her aim was to ensure that the school was inclusive for every pupil and met their needs.
"Mrs Robinson has championed equal opportunities and has demonstrated a long-term commitment throughout her career to combating racism within and outside of school.
"We have been and will continue to work with the parents and the school to agree a way forward. The local authority will be reviewing our involvement with the school.
"We do appreciate this situation has created a lot of anxiety and upset within the school community and we will be looking at how we can move forward together for the benefit of all pupils and the local community."
The school's new head teacher, Pamela Smith, said: "Meersbrook Bank is a school that has pupils from a range of faiths and backgrounds.
"We recognise that pupils have different needs and we, along with our local community, endeavour to reflect this in our assembly provision.
"The school has done a lot of hard work to develop good community relations and we are committed to reviewing how we can meet all pupils' needs within school by working with parents and governors as well as the young people themselves."
The legal requirements for schools to hold a "daily act of worship" vary around the UK.
In an English community school like Meersbrook, the requirement is for "a single act of worship for all pupils or separate acts of worship for pupils in different age groups or in different school groups" - meaning the sort of groups in which they are normally taught, not religious groups.
Most acts of worship have to be "wholly or mainly of a broadly Christian character" though others can reflect pupils' family backgrounds.
This basic requirement was established in the 1944 Education Act and has been re-enacted in more recent legislation relating to schools.
Parents have the right to withdraw their children from collective worship.
The statutory requirement can be lifted by a legal decision, known as a determination, by the Standing Advisory Council for Religious Education.
The Muslim Council of Britain proposes that in schools where most of the pupils have an Islamic faith background, the school should seek the power to implement more appropriate arrangements.
Part determinations can allow for Muslim, Christian and Sikh pupils to have separate acts of collective worship.