Yes, you can certainly split them to show the correct amount as clergy versus program coordinator. There is no need for concern to report the income appropriately and pay the self employment tax on the clergy earnings.
You may find you are unable to e-file with the same employer identification number (EIN) on two different W-2s. In the end splitting the income into two separate W-2s is the correct action for accurate results and you may need to print and mail.
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