You can't. You and the church erred by withholding social security. Turbotax will not recognize your W-2 as being a clergy W-2 and will not compute the self-employment tax correctly.
In my old church, for a while the treasurer transferred some of the pastor's salary into a holding account, and then paid the pastor's estimated taxes for him from that holding account, because the pastor (bless his heart) was not good with money and did not pay his own quarterly estimated taxes properly. But this was not reported on the form 941 as official withholding, it was the treasurer "helping" the pastor by paying his estimated taxes for him. (I also discontinued the process when I took over, for various reasons.)
The point of clergy tax treatment is that you are exempt from withholding and pay taxes as a self-employed person. There are certain adjustments that can benefit you in this situation as well. But by having formal FICA and medicare withholding reported on the form 941, you aren't being paid a clergy but as a regular employee, and if you tell Turbotax you are clergy, Turbotax will screw it up.
Separately, if your treasurer really did overwithhold social security and medicare (more than would have been correct for a regular employee), you can't get this back in Turbotax even if you are a regular employee. The church needs to fix this. The treasurer would submit amended form 941s that would result in a credit on your church's account. If you have other regular employees, the credit would get applied to their withholding until it gets used up (so the church pays out less and can give that refund to you). If the church has no other employees you can request a refund from the IRS after you submit the amended form 941s.
I think you and the treasurer need to see a tax professional to get this straightened out.
This may help as well, http://www.ecfa.org/PDF/2016-Preparing-Tax-Returns-For-Clergy.pdf
