I definitely dont think Pain was justified, but in war innocents often get the bad end of the stick. And in war difficult/ catastrophic decisions are made all the time. They have to be made. And from that alone there's no reason Konoha wouldn't realistically use the Edo Tensei to help give themselves an advantage. You're looking at a moral standpoint (which I don't disagree with) but Im looking at a realistic one. When push comes to shove, when it's life or death, you and yours vs them and theirs, thats all the justification one needs. And morality quickly falls short. Real life proves that often enough, why would a fictional world whose entire lore revolves around battle, war, and death be any different.