I agree that dynamic settings are a good thing. I can't imagine DMing without that approach.
But we don't know enough about the setting here to know what should happen. I use Umbran's approach of thinking about situations from the point of view, knowledge, and personality of individual NPCs, and deciding what they would do.
For example, who is the innkeeper? If he's an old "retired" (in hiding from his enemies) member of the Greyhawk Thieves' Guild, with connections to smugglers another gang of marauders, like one of the innkeepers in my campaign, he'd just assassinate the PC's by poisoning their food. First they'd get a whiff of it is when they are rolling d20s on their Fortitude saves for Dark Reaver Powder (DC18, 2d6Con initial damage, secondary for 1d6 Con + 1d6 Str in D&D 3.5e rules) -- good luck to them on that!
Also, who "runs" the town? If it's part of a feudal system, you can bet requests for assistance are going up the chain of command. They might send a Sheriff to arrest the party, or they might send more Knights, or they might send sneaky assassins or bold bounty hunters. I keep in mind that War Duke -- as impressively stat'd in Dungeon -- is mentioned as having a specialty of killing entire parties as a bounty hunter.
But I agree with Umbran, from a low level NPC point-of-view, or a bounty hunter's POV, revenge is a dish best served cold. Get the PC's when they are down, like returning from an adventure low on spells, and shoot to kill, as best the NPC's can try it.
If you're feeling nice, you might have a hot-head NPC mouth off to the PC's or threaten "you'll get yours" before the actual day of reckoning.
And if the "take down" fails, what happens next? If it's Points of Light, the PC's probably just have a completely hostile village, that won't let them into the walls (if there are walls) and will take the attitude of the Town Marshall in "Unforgiven" towards English Bob: "You know if I ever see you again, I'm just gunna start shooting, and figure it was self-defense."
If it's a more organized setting the PCs would be hunted outlaws, with wanted posters, people who refuse to sell them food because the penalty for helping outlaw is death, the works. That could actually be an interesting and unique campaign -- one where evil is "allowed" by the rules, but isn't the easy path at all!