Konohamaru won because he had rasengan and used it on a very lucky and sneaky attack. The entire time he was with Naraka Pain, he was squirming just to stay alive, and had his sensei cover him so he could hide.
Being completely theoretical since this never happened in the manga, Sakura could actually put up a fight against Naraka Pain, especially if both her fists and her feet are chakra-infused in order to make powerful attacks. We've all seen her fight against Sasori, where she demolished dozens of his puppets WITHOUT the assistance of Chiyo (remember, she was out of chakra and her arm was disabled). So we know she can fight fast-moving targets and still hold her own (of course! She's a chuunin!)
That being said, she still has to avoid Naraka Pain's grasp. That's the problem, but it's not a big problem. Once he grabs you, your chakra is depleted and he summons that statue to take your soul. So avoid his grasp and beat his ass! Remember that scene in DragonballZ where Android 19 had a firm grip on Vegeta, but Vegeta ripped his arm off to avoid being absorbed? Same situation here. He can't do a thing without his hands, and wouldn't you know it, Sakura has monstrously-strong hands.
