I was thinking about this and I'm not sure if I've cracked the code on this episode of if I've realized what everyone else already figured out.
My interpretation of Remedial Chaos Theory is that the episode isn't literally about the parallel timelines that actual exist in this world but rather how Abed perceives the world.
Abed is a student of character and believes himself to understand people on a deep, unique level. Naturally, his perception of how the group dynamic is affect by one person going downstairs for a few minutes reflects this.
However, Abed's deep understanding of how people is challenged later in season 3 with the episode Virtual Systems Analysis. The thesis of this episode is that Abed's seeming knowledge of how people function and how things will play out is clouded by fears and insecurities, like all good science fiction.
Believing that all the timelines are in Abed's imagination, then it makes sense how his biases affect what we see in the timelines. The timeline where Abed leaves is the saddest one. It's just a bitter, realistic timeline where none of the fun TV logic applies, where they fight and there isn't a happy sitcom resolution to this.
Most importantly, what triggers the darkest timeline?
Troy leaving.
The timeline where Troy leaves is the darkest timeline because it's not just about what happens for a few minutes, but extrapolating what would happen if they left the group forever. Everything falls apart when Troy leaves because he's Abed's best friend and potentially losing Troy is something Abed has to come to terms with in the later half of the season.
Ultimately, I believe Remedial Chaos Theory to be more than just a creative episode, but excellent foreshadowing of Abed's character arc throughout the season.
With this theory, then what does the ending mean? I've heard lots of different interpretations but believing that the episode is all in Abed's head, then I think it's pretty simple. It's not about how the group doesn't need Jeff or whatever. I think it's about the reality of what the episode is. The timelines present the scenario as a powder keg of unpredictable outcomes.
The timeline where Jeff gets the pizza is the real timeline and it presents the scenario as it really is. Just friends hanging out and having a good time.
This is how I interpret the episode and I'm not sure if it's a common theory or not.