Dragons fights are my favourite, I find the others perfectly boring. And, killing is what dragons are here for, so if npc get killed, well so be it.
I wouldn't mind if settlements didn't become ghost towns if you allowed dragons to kill NPCs.
This is easily avoidable though. Finish the Dawnguard MQ from start to finish without doing anything in between. It's too hard to police the Vampire attacks as they can happen on the other side of town without you ever noticing before leaving the city. Then you come back later and find seven ash piles in the middle of Riften's market.