In your case, I think you will get the right answer if you check the box for religious wages, then check the box for "pay SE tax on housing only." This is because his employment taxes on his wages were withheld by the church. Make sure that box 1 of his W-2 does not also include the housing allowance.
But the church is paying him incorrectly. Read below for more and especially read the linked PDF.
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Pastors are considered self-employed for income tax purposes. Typically, you will receive a W-2 with boxes 3-6 blank. Box 2 may be blank as well since federal withholding is voluntary and many pastors take care of it themselves.
You owe self-employment tax on your wages AND on the value of your church-provided housing (either a parsonage or housing allowance). The value of church provided housing is not subject to income tax however.
If your church is withholding social security and medicare tax in boxes 4 and 6 then they are treating you like a regular employee, not a pastor. You should not check the box for religious wages and in fact, you and your church finance person should probably both read this and then see a tax professional together. They/you are doing it wrong.
http://www.ecfa.org/PDF/2016-Preparing-Tax-Returns-For-Clergy.pdf
