You still owe federal and state income tax, you are only exempt from social security and medicare taxes (self-employment tax). You also owe social security and medicare tax on any income from non-religious work.
In most cases, joint filing will result in a lower overall tax for married spouses even when there is a large income disparity between the spouses.
Even though clergy are considered self-employed for some tax purposes, most pastors are common law employees and will receive a W-2. (You are a common law employee if you answer to a board, the congregation or the denomination -- someone that has the authority to hire and fire you and determine your working conditions.) Your W-2 should have your taxable wages in box 1 and boxes 2-6 blank. Enter your W-2 in Turbotax and check the box for "religious wages" on the page of special circumstances. You will be asked about your housing allowance and whether or not you have an approved form 4361. Answer appropriately.
Add your spouse's income and your combined personal deductions and dependents and determine the overall tax you owe or refund you get.
If all of your income is declared a non-taxable housing allowance, you will need to use the self-employed version and create a schedule C for yourself, because you can't enter a W-2 with zero in box 1. For the business code, use code 813000, this will trigger questions about the housing allowance and form 4361. Enter any side-income you get (cash from performing weddings, funerals, etc.) that is outside the scope of the church's written declaration of your housing allowance. (Remember that to be valid, a housing allowance must be designated in advance and in writing by your board or denomination.)
See this for more. http://www.ecfa.org/PDF/2016-Preparing-Tax-Returns-For-Clergy.pdf
