If you are clergy and receive a tax-free housing allowance (it is subject to self-employment tax but excluded from income tax);
then you are still allowed to take the standard deduction or to itemize your deductions on schedule A and deduct mortgage interest. (It sounds like double-dipping but it's allowed.)
This assumes your housing allowance is reported correctly. Your housing allowance needs to be documented in advance and in writing by your church finance board, and it must be excluded from your W-2 wages -- not listed as taxable income at all. There is no way for clergy to deduct housing expenses from their income, the housing allowance is excluded from income before it is reported, which is very different.
