How's this for a middle ground? Since NPCs are the vampires' food source, maybe they should feed and put them into a blood-loss coma instead. So a vampire attack would result in:
1) Dead guards - vampires target dangerous respawning NPCs actively and kill them, making subsequent attacks easier if the return before the respawn schedule kicks in
2) Comatose NPCs - the defenseless civilians are fed on (via a script?) and then left to lie where they fell until they recover 24 hours later.
This creates corpses (the guards) which makes subsequent attacks easier until they respawn. The NPCs are put out of commission but not permanently killed, creating a real inconvenience for the player (no merchants, quest-givers, etc. until they wake up) without breaking their game and no need to eliminate the attacks. The stakes aren't quite as high as perma-death, but there's a real motivation to thwart the vampire attacks, and they can go on ad-infinitum without breaking anyone's game. This also makes sense in terms of lore - the vampires won't lose their food source and exterminate every civilian in Skyrim, but they will effectively subjugate them if the attacks go unchecked.
Thoughts?