They could have also done a standard DNA ID check similar to the ones you see in CSI, etc. to see who was related.
One story about tracing Jewish origins noted that just about all Ashekenazem are descended from one Jewish woman who lived in early Medieval Europe. At the same time Jewish people are considered very closely related to virtually all other population groups and "isolates" in the Middle East, just like the Palestinians (as distinct from the so-called True Arabs), the Lebanese, a substantial part of the population in Syria and the Turkish coast.
What all of that means is population geneticists can use DNA to pin down most of your relationships even if you don't want to. Figuring out that it was Jewish people tossed down the well was an easy one!
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The other possibility is when the Vikings, or other plundering mobs, attacked a village they killed most everybody. If the village was mostly Jewish then they got whacked, if they were Huguenots, then they got whacked.
Difficult to absolutely say it was a hate crime but history would lend credence to the theory.