It just occurred to me that the problem might be that the church withheld your 15.3% SE tax and reported that all as withholding. But when you are a regular employee, you are supposed to pay half (7.65%) and the employer pays the other half, which would be why Turbotax says you are over-withheld. But that will also mean that the form 941s that the church filed will not match your W-2 or the church's W-3, and that's going to trigger an IRS investigation if you don't fix it.
That would also mean that it's not really that too much was taken out, but it was reported the wrong way, and you aren't really due a refund. You see to see a tax pro who knows about church and clergy taxes.
