Nick, your position is almost exactly like the one of my father in law. He's an atheist married to a devout dub too and I find your similarities in view to him both facinating and profound. I have argued with him about this same subject and he will defend the more tolerant Watchtower members. I can't help but commend you both for your exceptional empathy.
Although I disagree with you both, but sympathize with your positions. In fact I kind of envy your positions. Like you said the R&F are what gives the GB power not the other way around. Mind control, or youth indoctrination, has been used since history started being recorded. That's where the evil lies, not in the field ministry or kingdom hall, where the Rank and File pitch their way of life on their best behaviour, but in the household of a fully indoctrinated JW family. Your ignorance on that matter makes you nicer than Ex Jehovah's Witnesses and it gives you more tolerance. That's a good thing.
For every human tolerance will run thin and eventually completely fall through at some point. That point differs between people of course. You have been able to retain a connection, and even love, with your wife and has my FIL. Your relationship is a bright light among darkness and turmoil. Watchtower relationships are more often than not horrifying. You are wearing rose colored glasses, I hate to say.
You also speak about the intellectually stimulating conversations you have had with Witnesses. You say they respect you, but you are mistaken. They pity you, as a hopeless and bigoted atheist. They verbalize this prejudice as "differing views." They maybe even like you as a person, but they don't respect you as a person of free will and it's foolish to think otherwise, imo.
The Watchtower cannot be separated from the R&F because the R&F are not strong enough on their own. They are a weak and downtrodden bunch because of the their leaders. They drag themselves along their lives seeking a fantasy ending, but can only solve their problems, that they don't believe they have, by overthrowing their oppressors. Ninety nine percent of all evolved life is extinct. Most species don't make it no matter how hard they try and the members of the Watchtower society don't look like they'll turn an encouraging corner anytime soon. Being corgile with the Witnesses is just another stalemate in a long line of ineffective strategies.