You've got a big problem. I don't know how to get the SS tax back in this situation.
Typically, clergy are exempt from having FICA and medicare taxes withheld from their paychecks. Instead, they are paid their full salary and then pay SECA tax on a schedule C or schedule SE when they file their tax returns. In this case, once the form 4361 is approved, he would simply not file the schedule SE for this year and not pay the tax. He could also file amended returns for the past 3 years to claim a refund of past years SE tax (since the form 4361 is retroactive to whenever he started receiving pastoral income.)
The problem is that by withholding FICA and medicare from his paycheck, his church is not paying him as a pastor, they are paying him as a regular employee, and there is no procedure to get a refund of that. I think that what would need to happen is for the church to correct its tax filings. The church would need to amend its form 941s, and get a refund of the FICA and medicare from the IRS, and pay that money directly to your husband, and issue a corrected W-2 showing wages in box 1 and blanks for box 3, 4, 5 and 6. This would be moderately complex but doable for 2015 if they start soon. If your husband was also a pastor in 2014, 2013 etc and FICA and medicare taxes were withheld, it will be harder to fix for those past years.
Your husband and the church finance people (and the payroll provider if it is outsourced) should probably have a meeting with a tax professional in your area who is expert in clergy and church taxes.
This is also a good resource http://www.ecfa.org/PDF/2016-Preparing-Tax-Returns-For-Clergy.pdf
