The Oxford Concise English Dictionary defines autonomy as (1) the possession or right of self-government, (2) freedom of action. In other words, autonomy is the freedom to make choices according to the individual or group’s own principles and values. It’s freedom of conscience.
For Christians and New Testament local churches, autonomy is 100% conditioned by obedience to our Lord. In that sense, we have no autonomy. But in relation to those other than ourselves and Christ, we do have autonomy: the freedom to act according to what we believe to be the will of Christ.
We should view that kind of autonomy as precious, fragile, and a sacred trust.
We may better understand and value it if we consider it through a historical and theological lens. That consideration may also help us better understand how allegations of misconduct among members (including staff) ought to be handled.
Some Historical Light
During the Reformation, as churches were recovering biblical views of Christ, faith, and grace, they were also recovering a more biblical understanding of church structure and order. All reforming churches rejected the authority of the Pope and the traditions of Rome. Congregationalists went a step further, rejecting episcopal and presbyterian forms of church government.