I'm with jb on this. Historic preservation usually doesn't extend to something that can be a danger. Even is something is of historic value, it can still be demolished but if it is registered, then you need state approval but they can't usually stop these demolition projects.
Wells are a hazard for kids to fall in. A hole in the ground wouldn't have that much significance for preservation. Contact local authorities about proper well plugging techniques and plug it with a well plugging permit of course. Child safety is of utmost importance here. Add a recreated well house for historic purposes later.