Contributions are NOT deductible on Schedule C. 

Did she get a 1099 form the tax advice giving non-profit? If so, what did it show as the NEC amount?

The only way she could have taken any kind of deduction is to claim $10k income on the schedule C and take the $9k as an itemized deduction on her Schedule A Itemized deductions in the Gifts to Charity section. Which creates SE tax in addition to Income Tax, and if she doesn't have enough itemized deductions to bump up her itemized deductions to more than the standard deduction, kind of a lose/lose situation.