If it's any consolation, it's quite hard to spot those villages with reasonably normal vision as well...
I think your suggestion is a good one both visually and thematically. The only problem I see is how to distinguish them from the kota sites that already exists (at least some bugged sites resulted in a kota image and just a single kota rather than a village, due to some problem with fitting the village to the terrain. I believe that bug has been fixed, though).