Are you sure that it actually puts the social security part on schedule SE? If you already entered your W-2 and then indicate you have religious wages subject to SE tax on wages plus housing, the schedule SE itself should recognize the situation and only apply Medicare.
If you are working with Turbotax online, you probably can't see schedule SE to confirm this until you pay to file. You may want to use the desktop program installed on your own computer which allows you to examine all the forms and worksheets at any time.
Incidentally, just because you work for a non-profit doesn't mean you can have a tax-free parsonage, nor does having religious credentials if you aren't using them in your present job. You must be actively performing religious duties in your job, such as conducting worship services and administering the sacraments.
