A paycheck by any other name is still a paycheck, even if you call it a stipend or an honorarium.  She was an intern, same as thousands of other students in summer jobs.  Schedule C, and deduct the travel expenses if she was "away from home" and otherwise qualifies.  

"The stipend is not from Educational institution directly"  Nor indirectly, is my guess.  Schools don't make grants, they live off grants.  It wasn't from the Humane Society directly either, I bet.  But the source of the funds is irrelevant.