I once wrote an encounter for my home game with innocent bystanders in a tavern - but I asked my PCs to interact with them first, via an informal skill challenge. Once they had bonded with the NPCs, bam! Monster attack. And the baddies weren't picky about their targets (I made all the NPCs two-hit minions). I also gave my players the option of using a minor action to help the NPCs in getting themselves out (e.g. Athletics to boost them out a window - the NPC still had to roll a check). The result was chaotic, but fun. I'm not sure this would work in the Encounters setting, however.
Next week: BOSS FIGHT!