Fair enough. You don't need a zerg or even large group to invoke the consequences of killing too many NPCs. You're right.
Currently with the designed ratios of 30/70 PC to NPC, NPCs will automatically hold a lot of a servers infrastructure initially. Along with the sheer imbalance in the ratio, it is safe to assume NPCs will likely be the ones that do the "boring but needed" jobs of the settlement over the flashy optional roles players might pick. Tactically, it seems like the most effective way to deal with a settlement is to kill off it's NPCs and presumably watch it's town fold in on itself after losing over half of it's population. Whether your a village, hamlet, town, city or capital. Losing the majority of your population imo will most likely cause collapse. This also largely circumnavigates the CB system. While you can't use this method to directly gain their title, you can get the other outcomes of the CB system with it as well as make it much easier to actually hold for 28 if you wanted to CB. Aside from CB, I don't think it's good game-play for a settlement leader to have his settlement basically erased because of a design flaw in NPCs. No one wants to invest 250+ and then lose their settlement because their NPCs got themselves killed.
I do think a group that can take on and CDG so many NPCs in a sitting should have some sort of reward for their skill and effort, however, to me that comes in the form of pillaging the town for resources and the shiny things you pick up to sell. You get the massive loot, the name branding, and the glory. The loot allows you to reinvest into your group and grow as a player or organization, the name branding allows member growth as well as additional mercenary opportunity and the glory is bread and butter to why people fight for fun. As a merc, the word of mouth fear mongering is key to your growth, although you need to balance it to make sure you aren't a target but an asset.
CB should be the method of razing a town or taking leadership, not using NPC vulnerability to force a "guaranteed" CB. To me personally, that is just exploitation of their mechanics and NOT something you should punish a player for by taking their settlement because the NPC design.
My solution would be to only enable one death NPC during a CB, the one time this method of taking out the infrastructure should preferably be used because of the hoops to acquire a CB, while still a deadly tactic this allows the defending settlement some counter-play around the CB and trying to stop them from achieving a CB. The only CB condition that a settlement leader has arguably no counter-play for is wealth but even then, this is where you can use intelligence gathering to keep track of wealth of your citizens and the people around you. If someone looks like they are bill gates living in your settlement, be on the alarm until you can clear suspicion.
To me, that provides equal opportunity for both sides to attack and defend, instead of the possibilities leaving NPCs all-time 1 death has.