In SC this is simple - if he asks you to not carry in church you cannot carry in church. If he says you can carry in church you can carry in church. By default you cannot carry in a house of worship without permission from a "managing authority" (and you better have it in writing). His reasons do not matter as far as the law is concerned. This assumes the Pastor is the "managing authority" in the church, which would be REALLY hard to argue against.
In a state where carrying into a house of worship is allowed, then I would counter that this is a personal decision and is none of his business.
In a state where carrying into a house of worship is allowed, then I would counter that this is a personal decision and is none of his business.