Yes, you still select to pay self employment tax on wages and housing. If your church did pay towards your self employment taxes it should be in Box 4 as federal withholding. Box 14 should be used for the housing allowance so be sure of what you believe is true by checking with your church. If the amounts are correct, they need to send in a corrected W-2 for federal withholding. This is not a new practice.
Once you are clear on what should be in Box 4, and the church corrects the W-2, you can file your return with the correct figures before they actually issue you the form.
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