I've been answering minister housing allowance questions here for a very long time (and was a church treasurer for many years) and I agree with everything said by the Turbotax employee.
With one caveat -- if your wife continued in ministry (she was a minister performing sacraments and conducting worship services at another church), this might change how you calculate your expenses against the housing allowance. But I would have to research that because I have not seen that specific question before.
Remember that if she was paid a $15,000 housing allowance (not included in box 1 of her W-2), and her qualified expenses are less than $15,000, the difference is added back to her taxable wages, but if she had more than $15,000 of qualified expenses, there is no additional tax break or deduction. So you just have to demonstrate $15,000 of qualified expenses during the time she was performing ministerial services.
