In my experience, the child care people in churches know very little about kids. Usually its just a couple of teenagers. If yours is where the childcare is rotated among adults, then I would be especially angry that the behavior wasn't being dealt with. Are these kids actually seeking your son out to torment, or are they taking things from him without being taught to share, pushing him of line, etc? A lot of 2-3 yr olds have simply not learned to share...and that is the parents' responsibility. The childcare people should be following up.

Changing churches might help, but but so many of the problems are universal, unless you switch to somewhere smaller where the kids get more individual attention.
If the parents don't care, and the childcare people don't care, then that might be your only option to try.