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I agree with Charles, in that if I am asked if I am carrying( which since I OC most of the time hasn't happened to me) I will answer in the affirmative. I CC at church, because I don't want anyone's focus to be on me, or my gun, while there to worship. That said, I understand the OP position in that the question, should have been asked in a more private setting, and not while sitting in a pew. Many members of my church have seen me in public, OC, so they may,or may not be aware that I CC in church.

As a member if the praise band, I am up on stage during a large portion of the service. Our previous pastor, knew that I carry, and he had no issues with it. As far as I know, the only other person in our congregation, who knows that I carry, is our drummer, who just recently completed his LTC class and applied for his license. He plans to carry as soon as he gets his plastic. I have no idea about our new pastor's views on carrying, and have no plans to ask. I do know that there are other members who have their LTC, but as to their carry status on any given Sunday, I can't say.
The associate pastor, may have just been curious, but his lack of tact, and discretion, is unsettling. I agree with Charles, and others, who advise to just let the issue drop. If it is still bothering the OP, perhaps he can mention the issue to the pastor, and explain that carrying, is a personal decision and having to answer questions about it during the service, is off putting. He could then speak to the AP and perhaps help him to become more discreet about things. JMHO