As long as they are on church property or on private property, they can stay. For example, Christmas manger scenes put up by Christians on their own property or on church property are allowed. They are not allowed on public land.
Christians who complain that their city no longer displays religious Christmas symbols should decorate their front yards with manger scenes. Don’t expect government to be a witness to Jesus.
You are assuming an awful lot than there is to the 1st amendment phrase “Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof;”