It was a justified attack, such is war, and innocents die in such wars that is a fact.
She imprisoned whom she could and ordered the death of those who resisted in the slightest, these actions alone made the Alliance so much more interesting it was a realistic response.- The events in Dalaran; Jaina having captured/imprisoned numerous Blood Elves in her anger, which appears to still be the case according to Lor'themar's dialogue on the Thunder Isle. The ethics are questionable, but one can't blame Jaina with a clear conscience given the the perpetrators of Theramore's destruction are still unapprehended.
To be honest what purpose does honor have , it is a meaningless concept only those who can afford it cling to, once someone is pushed to the brink morals are thrown overboard, look at the blood elves they chose survival, instead of clinging to their high elven morals for example. Look at the humans who were turned into undead are doing now, the forsaken once were the core of the Alliance.In my eyes however, the Alliance is not defined, nor controlled, by personality traits such as the need for revenge; and the Siege of Orgrimmar is going to demonstrate this fact perfectly. We are not like Garrosh's Horde, which permitted the indiscriminate killing of men, women and children in Theramore, Gilneas and various other locations. If anything, the Horde are the losers in the Siege of Orgrimmar; whether they are serving Garrosh, or Vol'jin. What is the best one can say for the rebels/playable Horde faction? Well, the simple fact is that this story will in many ways portray them as hypocrites; for years, they proudly waged war with the Alliance. Not only that, but post-Cataclysm, they were the individuals who helped to make Garrosh's Horde a reality; and only now do they turn against their Warchief, when the tide is not in their favour.
The Alliance has to act before Garrosh becomes even more of a threat, before it is too late. They might not like the rebels, they don't need to forgive them and don't need to work with them in the future, the difference is after Orgrimmar has fallen, the rebels are still in a position to put up a considerable fight, which would lead to great losses ,as such and unconditional surrender is very unlikely. Varian himself says what he thinks of the rebels they are not allies they are a meatshield to save alliance lives nothing more nothing less, meaning their well being is irrelevant to him.Nazgrim being a raid boss in Siege of Orgrimmar, perfectly epitomizes the 'honourable' Horde; something that the rebels and playable Horde in this instance, are not. Nazgrim made a vow to serve his Warchief and, whatever the condition or state of his Warchief, and whether it means his own life or death, Nazgrim will be shown to uphold that vow, and his honour, in serving Garrosh to his last breath. He upholds his oath without reservation; and he will die for it. The Rebel/Playable Horde however, in this instance, are shown to express the ultimate humility. They ask the Alliance for help; and the Alliance have no reason to help the Horde at all. Why would they? After the destruction of Theramore, Gilneas, Southshore and various other places, the Alliance were perfectly at liberty to let Orgrimmar burn and the Horde rot; but they do not. The Alliance sets aside its faction differences, in the face of a corrupt Warchief who threatens war upon the world at large.
Atoning for what the sins exactly? War is hell, in war there is no justice, right and wrong, only death and suffering each side has their own morals their own justice. You speak of morality a concept that is ever changing what is right now was wrong several centuries ago and might be wrong again in the future. You treat justice and honor as if they were set in stone, but in reality they are not, they are ever changing.We will give the Horde something that was not shown to the Alliance under Garrosh; mercy. What will happen after the fall of Garrosh? The Horde at large will not only have to atone for its sins, but also remain morally indebted to the Alliance. If the Horde learns from this? Then perhaps there will be peace. If they do not? Then the lesson will no doubt be taught again.
Justice and wisdom are baseless concepts, each and every faction has their personal moral and honor code and different views on wisdom. The Alliance is in my eyes blatantly unrealistic to a point it can be seen as sheer stupidity. They are not acting reasonable, heck most lack the will to do what is necessary, just look at Jaina and Uther, they did nothing at Stratholme, which is far worse to what Arthas did in my eyes. The Alliance needs to stand its ground and should not constantly cling to honor and justice.Justice and wisdom; these are just some of the traits that the Alliance has come to be associated with, and they will not forsaken nor exchanged in favour of the Horde's "eye for an eye" philosophy. Whatever happens after the Siege of Orgrimmar will remain to be seen, but there is no reason whatsoever for the Alliance to deem themselves subject to some sort of injustice or bad story telling thus far; it is entirely in keeping with what the Alliance either is, identifies with or aspires to be.
Those who resisted in the slightest were put to the sword, like the shopkeepers for example, Jaina did what was necessary, but morally wrong.