This situation is not covered by Turbotax, and I haven't seen it come up before in the many years I have been volunteering here.
Generally, if your primary responsibilities are religious and pastoral in nature, and you occasionally perform other duties around the church (sweeping, keeping the membership list in a an office, other duties in a small church with no other employees for example), those duties would be considered part of your pastoral duties and would not be required to be listed separately with mandatory FICA withholding.
While it is true that if you had an non-religious outside job (school teacher, bus driver, etc.) you would be subject to FICA even though your clergy job is exempt, I have never seen that rule applied to split a pastor's income from the same church into two different categories.
I think that the splitting is unnecessary, and the church could probably pay you entirely under the clergy rules. Of course, you aren't paying me for professional advice and I don't know all the facts, so you may want to seek the guidance of a local professional. If it is determined that you don't need to split the wages into different categories, then the treasurer may be able to issue a corrected W-2 and get you a refund of the FICA and medicare withholdings from throughout the year, although this would require amending the form 941s and might need the help of the same professional.
If you decide to keep this arrangement, then Turbotax online probably can't handle it. To calculate the correct tax, you may need to use Turbotax Desktop version to make some manual overrides, and overrides void the accuracy guarantee. Also, I don't know if the e-file block that is coming from the combination of FICA and form 4361 is a Turbotax check that can be overridden, or an IRS issue that would prevent e-filing no matter what. You may need to print your return and mail it in, or seek the help of a professional.
