To Be Honest...
I always took that episode to be about them poking fun at the way people use the word "rape" in regards to discussing fictional pieces of entertainment from the their childhood.
Trey and Matt pretty sharply attacked Spielberg and Lucas before, in the episode where they keep going and tinkering with their past movies, but this episode I felt Trey and Matt were having some fun at fandom's expense too.
I can't remember all the details of the episode other than how melodramatic it felt. They really played out the idea of coming to terms with the rape and the ensuing grief, like an old TV movie.
It seemed to poke a little bit of fun at the fandom that uses a word like "rape" without actually taking into account what that word entails. I always thought all the rape scenes in the episode were meant to remind you that using a word like "rape" implies some brutal sexual imagery, and if you really want to apply that word to some movie characters from 70s and 80s, you have to be prepared for what it actually looks like.
I don't know... I can't go on and on about OMD. I like Brand New Day, to be honest, and I sort of understand the conundrum of separating Pete and MJ without killing or divorcing them.
The only flaw I had with OMD was that I thought Loki was going to be behind it, to tie together everything JMS was working on.
Flaws in the execution, eh, they come with the territory. I certainly don't imagine there is some scenario where Joe Q. and Steve Wacker are taking turns double-teaming Spider-Man in some seedy bathroom bar.