I don't think I've ever had a problem with "hurting" a character - I had a problem with killing them - but only hurting is not hard. I love the story more than my characters. What I do struggle with is not making my characters perfect
That falls into this category. Hurting them for me can sometimes be giving them a flaw. But I guess, I want the good guys to win, even though it's not as dramatic. Alas.