As a general rule, most missionaries would fit the ministerial exception, and it would be the rare employee where the mission would say that the person does not further its religious purposes. Persons would not be included under this exception if... 

In most states, and under the common law, communications with spiritual leaders are protected under a privilege called clergy-communicant, clergy-congregant, clergy communications or something similar. But when does it apply? Ministers must think through this before they start listening to confessions and other important communications.

A woman elder, a church employee, vehemently disagreed with her senior pastor’s position on a particular issue. She insisted on pushing her position until the Session finally fired her. Then she sued the church. But the Court agreed with the church that the government has no business telling the church how to manage its leadership.

Here is the church
And here is the steeple.
But does it belong
To the group or the people?

Church property disputes are painful and usually contentious. Usually, though not always, they begin when a congregation wants to leave the denomination, often over doctrinal fidelity. Because it is a dispute over church property, deep constitutional issues apply that may trump regular property law.

Although it doesn’t have much independent value as a precedent, a recent case is an eerie factual copycat of the recent U.S. Supreme Court decision in Hosanna-Tabor v. EEOC, an employment law case that applied the constitutional ministerial exception doctrine. Herzog v. St. Peter Lutheran, an August 2012 memorandum opinion out of the federal Northern District of Illinois, faithfully applies the Hosanna-Tabor principles to a similar set of facts.

The doctrine of church autonomy, which defines broad areas where civil courts cannot interfere with church decisions, plays an important part in First Amendment free exercise rights. On June 28, 2012, the Third Circuit issued a precedential opinion, Askew v. The Trustees of the General Assembly of the Church of the Lord Jesus Christ of the Apostolic Faith, Inc., supporting this doctrine. 

The disciplinary process for erring employees is intertwined with statutory provisions. You may become involved with the Civil Rights Division or the EEOC, even as a religious organization. Whether you can address issues internally and independent of government oversight depends partly on your policies and agreements.