I, personally, think it's a brilliant feature and it's little aspects (with potentially large consequences) to a game like this that make me want to come back and play- it adds another level of dynamism to the gameplay.
For example, I was playing Skyrim today and this scenario occurred:
I ran into Solitude down towards Proudspire Manor (in the evening), by the marketplace I ran past a hooded guy and kept on going- I then suddenly realised that the guy I just sprinted past had glowing eyes, so I quickly drew my crossbow, turned around and shot him just as he started attacking- some intense, brief combat ensued leaving the Ancient Vampire (disguised simply as "Traveller") and Jorn (a Solitude NPC) dead. I actually really enjoyed this scenario and found it to be a wake-up call for city wandering- scan the city environment for strange, unfamiliar folk and then act quickly. Even if the attack occurs on the other side of town (this happened to me in Whiterun actually- which, again, I found enjoyable) it is possible to kill the vampires before they cause trouble.
Ask yourself- would you prefer to return to a city environment where wandering around obliviously is not punished? Or would you prefer to keep this excellent feature which adds a new, exciting threat and keeps you on the edge at all times? I'd always pick the latter, if you pick the former- then you need to ask yourself why you are playing an RPG; the very nature of RPGs is that things are supposed to "go wrong", important people are supposed to be murdered and scenarios are supposed to be non-perfect.
I'm gonna respond to this since it seems like you've thought this through.
First of all, I'll say that you make an interesting point and that your scenario sounds cool.
My counter to that is that that's not what people are complaining about.
1 or 2 fatalities of useless NPCs aren't the cause of this. It's the pointless death of several NPCs and/or important and irreplaceable ones. You might enjoy that kind of scenario, but a lot of people are gonna be forced to babysit towns. There's also the fact that NPCs don't get replaced. The scenario you talked about was cool, but what if the blacksmith had been killed? What if it happens again? These scenarios and vampire attacks aren't a 1 time thing.