Have you checked the boxes on Schedule C for "Materially Participate" and "All Investment is at Risk"?  Those should trigger the SE income to be reduced.  I just did it on a test return and it works for me.

As a side note, I have heard that this link is a very detail publication about clergy tax returns, so you may want to glance through it for any questions that you may have.

http://www.ecfa.org/PDF/2016-Preparing-Tax-Returns-For-Clergy.pdf