Don't know when you took your CHL class, but the law has changed fairly recently.
You can carry in church unless there is a legal 30-06 sign. Your read on the law is correct, what your CHL instructor told you is not.
Part of the confusion is arising from the fact that you're reading a summarized version of the law. The "no posting" comment is not in the law. And the exemption which states that church carry must be restricted by a 30-06 sign is in a later subsection and refers to only SOME of the restricted sites in that section.
There is nothing in the Bible that even hints that carry in church is offensive or disrespectful, or anything else negative. If you FEEL that it is disrespectful, that's one thing, but you should understand that you're operating PURELY on the basis of your conviction without any Biblical backing that I'm aware of.