A specific review of all the relevant facts would need to be made to be sure one way or the other, but generally speaking, If considered an employee and not a licensed minister, you should withhold taxes and file a W-2.
If the individual is considered an independent contractor, you should file a 1099. What are the advantages of disadvantages? Unless the church has elected out of FICA (at the initial point of incorporation and filing its first information return), FICA taxes are paid by the church and employee.
On independent contractors, the church does not pay FICA tax.