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Perhaps I'm missing something, but if she doesn't currently meet the requirements of a minister (as defined in Pub. 517), she should be an ordinary employee. The employer should only be withholding the employee side of Social Security/Medicare, not both sides.
My guess is they aren't "Withholding X amount" but rather "reducing her pay by X amount" so they have the funds to pay the IRS.
(Not truly withholding - but what they'd do to have her get the same pay rate the whole time)

When it is W-2 time (and 1099 time) in a year, the OP will have to make sure everything is reported right.
Might even want to ask them if they can check what they'd generate for a W-2 as soon as she's no longer a regular employee.
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