If the amount was reported in box 7 of your Form 1099-MISC, then it will be reported on Schedule C (as mentioned in the answer above). There is not an option to get around it unless you want to hear from the IRS for not reporting the Form 1099-MISC.
In order to avoid paying self-employment tax or income tax on the amount you need to enter a business expense that is equal to the income amount reported. Go to the miscellaneous expense section and enter 'adjustment for stipend' as the description and the box 7 amount as the amount.
The end result is that you will not get a letter from the IRS for not reporting the information on the Form 1099-MISC, but you are not paying taxes on the amount either.
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