This is an interesting question. It's definitely true that in a lot of cases, the parent knows best. For example, my two year old will scream bloody murder every single time we brush his teeth. This is obviously hurtful to him, but we still have to do it. If we don't, he will ruin his teeth, which is a lot worse for him!
Still, we should never do anything that will actually harm the children. While it feels terrible for him to get his teeth brushed, it is not really hurting him. If it were, we would have to think of a better solution.
Overall, very interesting question. I suppose some cases of things that bring hurtfulness to the children could be considered okay, while other don't.