No, that's going to be an audit flag.
If the person was working in a non-religious job at a church, they are subject to FICA and medicare. Even with an approved form 4361, a clergy person working in a non-clergy position is subject to FICA and medicare.
If the taxpayer was a clergy person all along, just waiting for the approved form 4361, then the church should never have withheld FICA in the first place. And there is no tax procedure I know of to get it back, other than having the church issue a corrected W-2 and have the church refund the money. But this can be quite complicated.
The issue is similar to a case where a person's regular job withholds excess FICA and medicare tax. If you work 2 jobs, and your aggregate social security withholding is over the annual maximum, you can get a refund on your tax return. But if you work one job, and your employer over-withholds because they screw up, you can't use the excess SS form, you can only get a refund from the employer.
