Was the Art of S-Town Worth the Pain?

I don't see why this is relevant. As long as the journalist reports from within the ethical and legal boundaries of the profession, I don't think we can fault him/her if the subject doesn't like the end product. Very few journalists will give retroactive veto power to an interview subject, nor will they allow the subject to dictate who else may say what about the story. In the general case, in the absence of submitting the story for review before publishing, it is impossible to ensure that the subject will be happy with it. I don't think there's anything wrong with any of this.

2) "I would argue the subject of the podcast would consent" is not the same as consent. It's one thing if it's a public figure. The subject of this podcast was not a public figure.

So the first reason Reed gives for revealing John's apparent first lover is because John is dead and based on his assessment of John's personality, he believes John would not care, because again, he's dead. Besides the fact that there is obviously more at stake than your personal relationship with private information, i.e secrets effect your friends, family and enemies who are still alive, presuming that someone feels a certain way based on a few years of talking to them towards the end of their life is not an ironclad basis for an assumption like that. This reasoning is so shitty, that it almost makes the second reason weaker, as if Reed was kind of desperate to bolster his argument for exposing this somehow. The second reason is that other sources corroborated what John told Reed in confidence, so he feels that he can reveal it even though John told him not to. This logic sounds a little better than the first, but still, I'm not an expert in journalistic ethics, but I would venture to say that it's still a bit immoral to reveal that information via a third party, not least because they may be giving you a corrupted version of it. In my opinion it would almost be better to say "This person told me that John had a sort of boyfriend at one point early in his life", but not verify it with John's own off the record remarks.

Additionally, it doesn't realllly seem to add a ton to the story for me. I think that whether or not John had boyfriends early in his life could have been left vague and had the same effect.

As for the "church" stuff, again, I'm sort of at a loss. One thing that is for certain, as the article says, is that John intentionally did not reveal to Reed what was actually going on in these sessions. Again, I don't really know what's acceptable here from a journalist's standpoint, but to me it seems like he went a little overboard with it. By the end I got the impression, which I think was intentional, that John was getting something vaguely sexual out of "church" based just on Tyler's account. This is really dicey because John gets no retort because he's dead and it's clear he didn't really want to talk about it in the first place. I think that the pain addiction was an important part of the story, but again, I'm not sure it was worth the better part of an episode since John didn't want to talk about it when he was alive.

Anyway, I'm not saying that totally agree with the writer of the article. And as I said twice above, I can't figure out exactly how I feel about the whole thing. On some level though, it definitely made me a little bit uneasy, like I was eavesdropping.