I just think it'd be better if you'd been speaking to them and it's like a normal Zelda game and you think you're safe because it's a village, then later on in the game they suddenly attack you. Attacking you from the start before they've built up any ideas of where you're going to be safe in the game works to a degree, but wouldn't have the same impact.
If they were going to do something with the villagers, I'd prefer something like finding almost all of them frozen at the start of the game. Just frozen straight in their tracks. You meet a few who survived by hiding (or they were out of town or whatever) when Ganon cast his spell, one of whom is, of course, a wise old man. He tells you that their souls are trapped across Hyrule and he begs you to free them to bring life back to their owners. Then, by defeating certain enemies or bosses, or solving certain puzzles, souls are freed. Not only is this a storyline thing, you'd want to go find as many souls as you could as when the villagers return to normal, you can buy things off them or play their games or complete sidequests etc. Sounds more like Zelda to me than villagers attacking you too.