You can't claim a deduction for anything that you do not have basis in. Basis is (roughly speaking) the amount of already-taxed dollars you have invested in something. Consider a painter, they buy paint and canvass for $50, and create a painting they could sell for $500. If they donate the painting, the value of the deduction is only $50, because that is their basis--the already taxed dollars they used to purchase the materials. They can't increase their basis by the value of their time because they never paid income tax on it. Likewise for architect plans.
In the alternate, you could charge the church $50,000, report that income as taxable income to your business, and pay the tax on the income. Then, if you donated $50,000 back to the church, you could take a tax deduction for the cash donation (but only after reporting and paying tax on the cash income.) (Which would not even come out as a wash, since you would pay SE tax on the income but you could only take the deduction from income taxes.)
