The answer depends, in part, on state law where you are located. Because the answer will vary based on state, I will address the question under federal law.
First, different standards apply to ministers than everyone else. It is beyond the scope of this answer to determine whether an employee will be treated as a minister for employment law. I will note that determination of minister status for employment law is different from all other laws.
If the employee is treated as a minister for employment law purposes, then the church is free to treat the minister as it sees fit. The courts have determined that the relationship between a minister and his/her employing church is too sacred to allow for federal intervention. As a result, federal employment laws do not apply to that relationship.
If the employee is not classified as a minister for employment law purposes, then the church must abide by the employee’s employment agreement (if any) and its employee handbook. The church should act consistently with prior precedents in dealing with other employees. Further, the church must determine whether the employee is a member of protected class. The law protects employees from discriminatory employment decisions if the employment decision might be based on race, color of skin, national origin, marital status, gender, pregnancy, disability, or age. If the employee is a member of a protected class, then you must determine whether the decision could be partly a result of unlawful discrimination. You will need the assistance of an employment attorney to evaluate the risks.
Many states create additional protected classes of workers.
Finally, the courts may treat a long term suspension as de facto termination. So any employment decision should be consistent with termination of the employee.
You also asked about documentation. There is no fixed formula. The more documentation the church possesses about the situation the better. Only an attorney can determine whether it is adequate under the circumstances.
This decision should not be made without consulting with an employment lawyer from your state who is also familiar with how the church’s unique status impacts the application of employment law.
This answer was prepared under the laws in effect as of October 31, 2009. This answer is not legal advice, just legal information.
For more information on staffing-related questions, see Pastor, Church & Law by Richard R. Hammar.