Home Office deduction disqualified

In the past I have received a 1099 for income as a contract worker (or similar title) in temporary church ministries.  Because I wanted to be sure to receive credible evidence that I had arranged with a church to receive this income as housing allowance, I requested a W-2 on which housing allowance can be listed (box 14) instead of on a 1099.   Although the underlying reality remains the same, I have discovered that my self-employment income is diminished (without a 1099 to enter as self-employment income) to a point that my cost for a home office is disallowed.  Is there a way to end run this situation legitimately and legally?   

 

NOTE: I prefer that those answering know the particular nuances and idiosyncrasies of ministerial self-employment taxes.  Thanks for your help!!