OMG. You guys REALLY don't see how absolutely stupid siding with Harkon would be? Really?
Let me repeat, a handful of vamps against an ALL OUT ASSAULT from not only all of Skyrim, but Cyrodil, Hammerfell, Morrowind, Elsweyr, Blackmarsh, etc. EVERYONE, EVERYWHERE who wasn't a vampire would be at risk. There is no way at all in any fathomable stretch of ANY scenario that the vamps could come out on top. None. Castle found. Here comes the invasion. You're there, stuck on the island, surrounded, and your ONLY resources are those that you currently have. No resupply chain, no way out, and hundreds of thousands of invaders endlessly pouring in. That's a no-win scenario. Read it again, there is absolutely no way you could do what Harkon proposes and come out on top. Hence, it's stupid, hence, not an option. And you're faulting the developer for not allowing you to be a complete moron and not dropping you into an unwinnable situation as a result of that stupidity? Essentially ending your character. Forever. Done. Please.
Your tenacious assertions of Good triumphing over Evil would be inspiring, if it wasn't sooo cuuute...
To think that the cattle would ever think themselves greater than their masters...makes me smile.
When are the wolves ever concerned what the sheep think? The wolves care only when the wolves feed, when the wolves instill chaos in their minds and fear in the sheep's heart, right before the wolves rip the still beating heart from the sheep's chest. At least that's all my character Raven has to say on the subject, 
...but seriously.
I respect your point of view. I just choose to disagree...because it's fun to watch your head explode

I can almost hear the gears in your head grinding.
Delving into a dungeon filled with zombies raised by a lone necromancer is fairly common place in Tamriel. At least it was in Cyrodill (cerca TES:O).
The way these Vampire Lords are presented in Dawnguard leads me to believe that each has at least some rudimentary necromantic skill. It wouldn't tax the imagination much to think that the older VLs in Harkon's court would have greater talent than you (being that your still green to the ways of being a Vampire Lord). So raising an army of undead and skillfully placing them for ambush wouldn't be so hard.
Northwatch keep is fairly defensible. Filling it with undead shouldn't be too hard. It's already filled with Thalmor so killing and raising them any one Vampire Lord could do. Better yet, turning them as Vampire Thralls might be the way to go, and yes there would be time enough to do that. There are always greedy, power hungry people so it wouldn't take much to find one or two within their ranks to turn into Vampire Lords to lead that rabble. Sure, it's not a permanent solution, but if for every one Vampire that is killed they take 10 with them, that's 10 more bodies to be raised in their defense.
I'm positive that there would be groups and covens that could be convinced to come to Harkon's defense, and still others that could be "persuaded". If I were Harkon I wouldn't fill my castle with them, instead I'd send them out into towns and villages to kill or turn men, women, children, in their sleep. That would slow Skyrim's momentum if not completely demoralize the people. Sure, there would be those that would be emboldened and driven to retaliate, and it would be these that are picked apart as they march on the castle. Like a pack of wolves slowly picking the herd apart, one by one. They'd be lucky to arrive with half of their forces in tact.
How many times do we come across a story where one lone Vampire has existed for years within a community causing all sorts of chaos before they are discovered, or you (the PC) are brought in to discover them? How many of these quests result in the town raising up against that Vampire? In how many do the towns sheeple lean on you (the PC) to take care of their business for them? You say that the towns and villages would be hunting the vampires down in their caves with torches and pitchforks, I say they'd be too busy looking inward, making sure their "trusted neighbor" for the past few years wasn't in fact one of "them". Not every town or village would fall, but I think a vast number of them would quickly become ghost-towns before anyone knew what the hell was going on.
[Edit: Ooo! and lets not forget that a sudden and skillfully timed/planned invasion of Solitude (City and Hold) along with Markarth (City and Hold) would be in order. Solitude would be overrun long before they could put up a proper defense. Only a few unlucky may be able to hold up in the Blue Palace, but eventually they'd all die or be turned or enthralled.]Remember also, there are other factions of Vampires throughout Tamriel, and not just Harkon. They may not get along, but the
blood sun* might be the factor that temporarily unites the clans...so it wouldn't be all of Men and Mer against Harkon and the PC. Harkon may be crazy, but I don't think he's a moron. He wants the power to rule over his cattle and not hide in the shadows. He wants to visibly sit upon his throne and be worshiped, not wipe out all of man and mer kind. He just wants his turn to play the Game of Thrones.
* just to clarify, I call the "blocking out of the sun" a Blood Sun, only because I think it better fits. The sun isn't truly "blocked" or "blacked out". Light still gets through, though diffused and tinted red. Iit may severely affect the world in horrible and unforeseen ways, but I don't think the world would come to an end. Men and Mer would still survive. But that's just my opinion 