The Purge is a great example of the playerbase not being able to actually handle morally grey writing, really morally grey writing, in the few times that Blizzard actually does it. It’s no wonder they need to be hamfisted one way or another.
Jaina randomly killing civilians is a bug, it has been said as such, but going after every Blood Elf in the city to imprison them was on her command, and thus any deaths during this would fall on her and Vereesa, this much is entirely true. So yes, Jaina is responsible for any deaths during the so-called Purge. That said, while any number is pretty not great, the deaths couldn’t have been too egregious, since all the blood elf NPCs from Wrath are right back there during Legion, and even pre-Legion during the patch, when it was under Jaina’s command still.
In context, the Purge of Dalaran is basically the only actually morally grey thing Blizzard has ever written. This is mere months after Theramore has been wiped off the face of existence in EVERY reality, and when the Divine Bell was stolen, there was complete and total evidence that some of the Sunreavers had helped to make that happen, using Dalaran’s portal network. On her watch, in fact, because she let her guard down.
Imagine then, what that could have resulted in? Dalaran’s portals are linked to every major city, and an unknown number of Sunreavers had used that to put a powerful magical weapon right into the hands of the Horde, a Horde that had used a mana bomb in recent months and could very well want to do so again. Let’s be clear, the only reason the Sunreavers didn’t become outright villains is because Anduin stopped Garrosh. If he hadn’t? It could have spelled the end of the war, and anyone who stood against the Horde Garrosh envisioned.
The Purge is morally grey because the circumstances made it impossible to do anything else, in the face of the possible consequences for doing nothing or moving too slowly. In context, we’re talking the potential deaths of thousands, hundreds of thousands. Jaina gets fragged for it, but what about Lore’themar? Those are his people, actively working to violate Dalaran’s neutrality, yet he knew nothing. If Garrosh had made his supersoldiers with the Bell, or used the Sunreaver agents to sneak a mana bomb into Stormwind, what would he have said, “Oops.”? Varian chiding Jaina because he was planning on having the Blood Elves join the Horde is completely inane, because it was a group of blood elves who actively tried to help the Horde turn the tide.