One vitally important point to make her fully conscious of is why she believes it is the truth. She does not know the doctrine too well, yet is satisfied to accept it is the truth. That sounds like most people from most religions. In other words, she believes it is the truth because she was raised as a JW. You can subtly make that point in numerous ways and occassions.
For example, when watching the Mormon documentary it would have been a perfect opportunity to ask, "if you had been raised a Mormon, would you believe that was the true religion?" It will create some internal discomfort that will then always play on her mind when she is hearing things that make her question the organisation.
I also recommend telling her you do not want her discussing Armageddon with your children. It is traumatic and not suitable for children. It is shocking for them to have to contemplate destruction of such a nature. That will make your wife think about Armageddon and can then lead to the conversation that it is not logical for your children to have to think all their friends will soon be killed by God just because their parents are raising them to believe in a different religion.