That episode was really bad. Very uncomfortable. I can't believe how bad the stuff you cut must have been. Only episode of a podcast I ever clicked the dislike button for. Rather than just complaining I'll outline WHY I feel this way.
1 - The laughing at the terrible parts. I know you guys address this in-episode, but the problem is that it sets the wrong "tone". If you approach it with a "wow this is awful" tone, it will appear 'less' awful VS laughing at it, as there's less of an emotional cliff edge. I don't think either of you are bad people, I've laughed at far worse, but from a podcast making prospective it was too far.
2 - Too much 'dwell time' on the terrible things. The episode where folks got murdered tended to deal with the murders rather quickly and moved on to other parts of the story; and despite those other parts being set ups for further murders, the fact you didn't dwell on talking about the actual act itself meant the listener wouldn't spend too long in that state of discomfort.
3 - similar to point 2, but parts of the discussion seemed aimless. Simon's comment "was this all just a set up" RE: the cake thing, I think hits the nail on the head. You guys set out to tell the story of girls jumping out of cakes, and as such, the "sidebar" that was the trial, wasn't as strongly narrative driven as it could have been,.
I also hope the story you cut does eventually make it on to the podcast. When it does, you need to focus on everything but the rape. Focus on how the people involved felt they could not report it properly. Focus on how those who knew the accused helped to cover it up. Focus on how things like this (very likely) happen more than we ever hear about. Focus on how one or two bad seeds can drive others to bad action. Focus on how the un-enforced banning of booze lead to this; should booze have been more strictly controlled to avoid this, was it inevitable that they'd drink and the lax enforcement thus caused only lead to further problems, or would they have never committed these crimes if they had not been drinking.
You guys have dealt with uncomfortable stuff well in the past; and I'm confidant you can do so in the future. This is simply the one time you guys didn't quite get it right. I still like the show and am about to fire up the next episode right now; but wanted to give my thoughts on how to avoid these sorts of things in the future.