I breathed a massive sigh of relief listening to this episode. I had a lot concerns while reading the story and you raised pretty much all of them either in the recap or the discussion. Like Glenn, I was excited to read this because it sounded like exactly my sort of thing, but it fell completely flat in the delivery. I was worried that I was just taking a comic story way too seriously (and I'm willing to concede that there's an element of that), but you're right that the world has moved on a lot since this was published (and again like Glenn I would have lapped it up at the time).
That said, I think (and hope) there's still room in the world for alternate history stories, albeit they need to be constructed more carefully now, in a way that respects the reality of events. As Brandon pointed out, more ridiculous concepts and obviously "not real history" stories are probably going to work better. "Ancient Aliens" is a concept I have a lot of issues with as a historian, but fiction seems like an acceptable place to explore the idea. Maybe that's just a youth spent watching Stargate SG-1 talking though.
For me, that's the root of the problem with this story. Not just that it trivializes genuine historical tragedies (both personal and large-scale), but that the alternative "facts" presented are themselved fairly trivial for the most part. Again, this is something you brought up in the episode: where are all the aliens? Where are the medical conditions that need to be covered up because the truth would be too horrific for people to accept? Conditions caused by bugs we've never heard of are, to be frank, kind of lame. To take the point a little further: there's absolutely no reason this guide (if it was real) wouldn't be accepted and used by every medical professional and organization in the world, and no reason these "facts" wouldn't be publicized. I guess you could argue that there's an implied undercurrent of some kind of conspiracy to cover up these events, but why? This "obscure medical history of the twentieth century" is nowhere near weird enough to justify its supposed obscurity.
Not much else to say really. I'm just about intrigued enough to read some of the other entries in the collection, but with far lower expectations than I had going into this one.