I'll fill in a few unknown parts of the story from ulterior resources:
* When you see something wildly out of its time like that, you're usually seeing evidence for one of two things: a super-gizmologist good enough to engineer a new solution, or someone with enough farmemory to recognize the problem and reproduce a solution. Another source of exceptional input is spirit advice, but they don't usually tell people to build walls with rocks, so I rate that much less probable.
* And the villagers miraculously listened, which is rarer than you might think and why these things often appear in isolation. So they had not just one smart and/or mystic person, but the group itself was especially fluent in one or both of those things. That speaks to the likelihood of their survival.
* You can't keep back the sea, but there is one thing you can accomplish by fighting an impossible battle: you can buy time. They may have known it was a lost cause -- it's not hard to recognize that if water keeps rising, you are going to lose -- but if they had a Plan B which took time to develop, such as preparing another village site elsewhere, then the wall likely served its purpose.
So if I were an archaeologist, I'd take my trusty tapping pole, some portable scanners, and a good handful of interns and sweep straight inland from the village and along the river, looking for that Plan B. If I could identify where on the river the rocks had been taken from, I'd use both that and the village as reference points to search for the subsequent site, because people who build walls are prone to repeating certain geometric patterns.
Also, don't forget that this is us. A century or two from now, most of Earth's great cities will be underwater, because so many of them are right on the waterline. You know, like that neolithic village. Here's what it would look like if all the ice melted, but they're underestimating the speed that can happen, and it won't take nearly that much to sink the cities.
Now would be a good time to make a Plan B.