Yes, you need to do damage control now. She is upset because you set her up for a fall. You knew about the change of doctrine, but she didn't. You made her say what she had been indoctrinated to say, then showed her that she was made a fool of.
I suggest you apologize to her and acknowledge that you set her up. Keep apologizing until she accepts that you are really, really sorry. She was not treated like your other half. Treat her the way you would have wanted to be presented with this new, disturbing information.
Next, explain how much you want to be able to talk about this subject with her, that you are justifiably angry that the organization keeps changing important doctrine and it has stumbled you and made you lose your faith in them. Then, start over, you know how to take it from there.
Remember, your wife needs and wants you to LOVE her. Love her by being kind and heart felt when presenting your views. You are right, and hopefully when she cools down, she will sympathize with you. That's what you want. We women respond to our husbands when they make us feel loved, honored and appreciated.