"He is the pastor of Liberty Baptist Church. He is not the owner. Since the very beginning he has been a 1099 individual."

That doesn't make it Correct treatment, though.

"Due to his actual profession, as an engineer,"

He likely should get a W-2 from the Church, as well. Just because he already has a different employment position, doesn't affect the classification for the church relationship.

"he purchased and built the computer equipment. Liberty Baptist did not reimburse him."

You have to determine the facts and circumstances. You cannot claim that is for the Church, when he doesn't own the church and is not an employee of the church and did not get reimbursed by the church. If it is at his office, it is his. If he used it for his business, it is his.

This church and this person need some worker guidance.