I just did the alliance-quest myself (Taking my time with the reps instead of spamming dailies, burning out and then going "ZOMG I HATE DAILIES!!!" on forums :P ), and from my point of view there is little evil stuff going on, Jaina kills Aethas' personal guard, she comes in and they're in battle stance, must have been expecting a fight, why would innocent people expect a fight at that exact time?
Then purging the city, Jaina goes in circles along the main street, teleporting people (Presumably to violet hold to sort good from soon-dead), not killing them outright, the quest doesn't require killing of panicked people in the streets, the only people you end up killing are people who are looking for a fight (The sunreavers have a way cooler inn BTW, HORDE BIAS!!! :P ), the vendors are pretty clear about their intentions, as is the banker...