Thank you Alas for the very thoughtful reply... you've articulated a lot of what I've been thinking the last ~two weeks but have been too afraid to bring up to my wife.
It's a conversation that needs to happen and I probably should just bite the bullet and bring it up as she did a few weeks ago about taking him again.
I don't think it's unfair to say that if he's taught by the LDS church these lessons that I can teach him where I'm coming from too, and while I don't know what that actually looks like, I feel like it's the only fair way to do it.
My biggest thought that I can't really say to her is: How can you want to teach our kid something that you know has problems to the point where you can't even talk about it with me?
I can't say that, of course, but it makes me think of my sister-in-law who has her only kid on a mission right now even knowing that her sister and brother-in-law have left in recent years because they've found out it's not true. Instead of asking either one of us what is going on, she doubled down and make sure her kid went on a mission. That's a very common response, but it is that line of thought that makes me feel like it's worth the fight to be able to teach him now so that he doesn't get to that point himself.
Anyway, thank you for responding when you did - it's the reminder that I really do need to have this conversation to figure out how to do this if she wants to start bringing him again soon.