Actually, you're not doing a good thing by killing her, but you are doing a necessary thing. I feel sad every time I have to kill her, and that's how you're supposed to feel.
The powers that be (the Priests) consider her to be evil, not because of her deeds (which are noble, taken out of context), but because she has defied God by embracing a Demon Soul and using that power to help relieve the suffering of others. In truth, this makes her the most noble character in the entire game, but according to the Priests, this does not excuse her blatant "debasement of the Lord's name" (or what they claim is defiance of God; we never actually hear from God on this matter).
In fact, Astraea is doing nothing different from what you are doing: fighting fire with fire, by using the power of the souls arts to combat the demons with their own weapons. She is no more evil than you are, and that's why you feel guilt. If you haven't already figured it out before that scene, you now know that your character is a hypocrite… and so is the Monumental, but there's no way around it. In the game's final scene, you have to decide whether to give up your power for the greater good, or to be selfish and keep it for yourself. Either way, you did some nasty things along the way that you'll have to live with. Do the ends justify the means?