What if you kill in self-defence? What if you believe that a person has brought about their own punishment? All magic, dark and light, is what you make of it. You are not automatically good or bad because you use one or the other. So, Voldemort's ritual. It itself was not evil. It was merely a tool, a function. The use he put it to was - well, certainly repugnant (I hesitate to use the word evil even in the case of Voldemort). As for transfiguration, or charms: you would expect it to hurt. A lot. Lupin's transformation's hurt him, and they are to a large extent a more primeval and uncontrolled feature of transfiguration.