I think that he attempted to do this with his first podcasts before his leave of absence. But now, I can't say that this is his agenda. I think that in his first podcasts (before his leave of absence) he also attempted to answer his own questions. The Blacks and the Priesthood podcast is an example of that. Also, his interview with Bushman among others. It shows a member who needed answers to his questions for the sake of their own testimony.
I think that his podcasts are different now.
You're probably right. When Mormon Stories was in its infancy, John regularly promoted ideas later formulated in his website, StayLDS.com. It should be noted that StayLDS also got some flak at a FAIR Conference a few years back, but I digress.
But some time in 2010 or possibly even earlier, John made the decision that "staying" in the Church isn't always the best option for some people. That's the impression he left me when volgadon and I had lunch with him that summer. So there's been a gradual moving away from the "why I stay" Mormonism to the "why I leave" kind of Mormonism. Some time last year, if I recall correctly, John was called in for a meeting with his Stake President (which caused quite a stir in the Mormon Stories community). As far as I am aware, no disciplinary action was taken (and I'm not going to claim there should be). What happens between John and his ecclesiastical leaders is something personal to him. I think the Church is likely aware of the potential backlash associated with disciplinary action being taken against (somewhat) public figures, so that might be a reason why there hasn't been a crack down on self-described "Middle-Way" Mormons in a while.
Though I really have no formal affiliation with John, he's certainly helped many people understand how faith is often a journey of sorts. I don't feel judged by him personally for being an active, believing Latter-day Saint, and in some ways he's helped me be more personally tolerant of others in their respective faith journeys. Obviously I'd rather see more people return to full fellowship, but that doesn't seem to be the case most of the time. It isn't uncommon for two people to approach the same piece of literature or scholarship and come away with two competing perspectives.
I can't say my faith is intact as it was when I was a missionary. Arrington, Bushman, Barney, Ostler, Faulconer, and several others have certainly molded that faith into something else - likely a much more postmodern view of things. I'm happy with that change. Others don't always make the transition as smoothly. For some, that turns into disbelief all together. After subbing a Primary class a few weeks ago with my wife, I'm still convinced that Mormonism is the right path for me. The little things that rang true to me as a child still ring true now. I'll readily admit that I haven't always been the best example. I've tripped up, stumbled, and even fallen on my face more than a few times. I wish Mormon Stories (as a community) was more welcoming of people who - when recognizing their imperfections with regard to faith - still happily stick around.