I think that making them "weaker" or "devolve" into something else rather than making them stronger or outright killing them is the more sensible solution.
By weaker or devolve I don't mean necessarily physically weaker. A vampire that lacks feeding for a long time can perhaps become extremely sensitive to sunlight, or become too paranoid or crazy, or become a savage beast by losing it's mind, even physically change into something akin to an animal (like the vampires of the Priest or in Soul Reaver), or a rooting body (basically a zombie with fangs) or anything you can think off.
On the other hand it would be cool to have vampires become either less or more dependent on feeding as time goes by, this could make either extremely resilient vampires as they get older or the other way around, where vampires have a hard time getting too much old because their ever increasing need of blood will weed out most of them to become feral creatures (perhaps more easily killed?), and only a smart and skillful minority could manage to survive (or surdead?) in the long run. On both cases to keep getting older the securing of continuous feeding could be needed, either by terrorizing villages and killing competition (a solitary life) or forming groups, clans, kingdoms, civilizations or whatever to watch each other backs and ensure control over large amounts of population to feed upon.
Vampire fortress are not exploits, they are simply not challenging enough yet. In all modern "folklore" we see that vampires, as much evolved they are, still need to feed upon humans. Take day breakers for example, in that movie the vampire population got out of hand so bad that they ended up ruling the world, but need to have human farms a la matrix to harvest blood for everyone and even then food is scarce.
The issue with vampires is that they are apex predators, and as such their numbers must be necessarily smaller that the number of their prey in order to keep them all "alive" (or happy, or whatever). For them to from up groups, bands, fortress, civilizations, they need some strict behavior code (so they don't multiply beyond their sustainability or kill each other) and they need a food supply. In the case of "sophisticated" vampire societies they could even reign over a no vampire civilization, eating from them without actually diminishing their numbers.
A perfect example of what we could look for in this case is the one of Sylvania from Warhammer 40k, there vampires are more or less scarce, their armies are mainly composed of zombies and skeletons raised when needed, mercenaries and even human citizens of their lands. They don't outright exterminate the humans, they just keep them under their power and feed upon them on necessity. In fact humans under their reign are marginally happy, since they don't collect much on the sense of taxes (beyond the occasional peasant for dinner), provide plenty of security for them (few dare to enter a zombie/vampire/skeleton/werewolve infested land to plunder) and basically mind their own business.
On the other side right now DF lacks (for the time being) something that would definitely keep vampires in check in every universe. Vampire hunters. From Simon Belmont to Van Helsing, they all have been the ultimate terror to vampires. It remain to be seen, once is implemented, how guilds, groups, religious sects and orders would affect the world, but I have no doubt there wont be a lack of vampire hunters (that would also hunt other assorted monsters). That could be the crucial element of balance to keep vampires in check.
By having one of such guilds on your civilization or laying around in a neighboring one, you could expect regular visits if there is anything suspicious, random trials a la Spanish Inquisition (but they you can' expect ok?) or perhaps you can even call them for help with your liaison once you suspect something funny is happening in your fort. But this could go the other way around too, if you intend to make a vampire fortress then they could be added to the list of sieges or even "excommunicate" you from your civ if they fail to clean the fortress either by action or inaction form your side, basically making everyone and their grandmother you enemy.
Thoughts anyone? (Beyond what a bunch of text)