So this becomes a nature vs. nurture debate. Would she actually be different? I think she would be to an extent at first, however I do think eventually she would see her stepmother for what she is and probably turn against her. It might manifest differently, whereas she ran away originally, she may actually face the Evil Queen and try to wrest control of the kindgom. I think her inherent good nature would win out, though it may be tempered with more pragmatism and less idealism. She might make a great Queen that way.
Interestingly, that leaves the question, who does become ruler after the Evil Queen dies? What is the story told to the subjects? The Evil Queen was basically smote by God, so I don't know how well that would go over. Then again, the people were probably happy to be rid of her all things considered.