I'm not sure if this is correct, but can this sentence be interpreted as "You are from both villages"? The दोनों seems to be a bit of a misplaced modifier here.
I think that "You are from both villages"≈तुम दोनों गाँवों से हो। Since there is a single village in question,here "दोनों "refers to two people.
Also, a person might put stress on "both" if he/she expected only one (or none) of them to be from the village.
The sentence is correct in relation to how the words are placed. The only way to really know the difference is by listening to where the stress is placed. In the actual scenario, there is more stress placed on "village" than on "both", while in your scenario, there is more stress on "both" when compared to "village".
I agree.... And hindi language is a very contextual language, so depending on the context the meaning could either be two people or two villages.
But as the ragingfire said You pay attention to the intonation and stress.
"Both of you are from village" should be accepted. Here the sentence doesn't mean any specific village