The phrase "to leave the church" means that someone has decided to stop being a member or participant of a religious organization called a church. Full definition
Many people leave the church because they look to other human beings to be their guides and inspiration; when that person or persons fall short of expectations, they become disappointed and leave. (religion.blogs.cnn.com)
In fact, many people who suffer from emotional disorders have to leave their churches in order to heal. (nakedpastor.com)
Too, some people leave the church because they choose to engage in practices that are sinful or harmful. (religion.blogs.cnn.com)