Probably the bedrock part of my process is looking for a puzzle to solve - how do I explain something and make it logically work? You’ve given that challenge here, so here we go. 
My first personal “rule” on a Sliders story is “don’t change the world”. I personally didn’t like the idea that the Sliders would come in and radically change human history. It works in some of instances (like “Last Days”), and it can even work on a smaller scale (like “Weaker Sex” where Arturo could be running for a smaller office like Mayor or City Councilman). But keep the stories small and personal. Local level.
My second “rule” is that the Sliders should be the stars of their own story. Looking at especially the later years, too often the Sliders would land on a world and help random person X with random problem Y. The Sliders would be reduced to facilitators of some stranger’s story arc. I suppose that too can work occasionally, but I don’t like it at all for a show such as Sliders.
Sliders is a survival show. Though often ridiculous and regularly frustrating, Sliders is the story of four people trying to simply hang on until they can make it home.
Those rules in place, I then ask a question - “what is reality?”
There is no set definition of reality for anyone; and even in an individual’s life, the meaning shifts based on the circumstances. Thinking on that question today, the first thing that came to mind was a strange phenomenon I’ve experienced and is talked of in movies. When we go on vacation to an exotic locale surrounded by strangers, we become the person we want to be instead of the person we are. It’s temporary - you change back as soon as you go home; but while on that trip, you are taking a vacation from yourself.
Now with a rough, basic premise, let’s look at the basket of alternate history ideas (something I’m constantly building and have been posting here). For this idea, we’ll use the most recent I posted - “Bubble World” (where people are segregated based on how they think and feel).
So how can this fit together? The Sliders land on “Bubble World” noting they are going to be stuck here for weeks, and one of them (probably Bennish) says something pretty tame that deeply offends the people they are talking to. A heated argument starts; people are running for help; authorities arrive, and before we can grasp what’s happening in the chaos, Alli is injected with something by the authorities and blacks out.
Alli wakes up in a “re-education” center. Alli is to be taught the “correct” way to act so that she can re-enter society as a productive person. This training can also be our vehicle to exploring the history of this world. I would recommend a mix of various ideologies as the “correct” idea so that you can hold as many viewers as possible. We’re often not as far apart as we think.
As part of the training, Alli is put into something like a therapy group; and she is surprised and irritated to find that she has been reunited with Bennish. In talking, Bennish shares some of his back story; and the longer the episode goes, we begin to notice that Bennish is a better person. Alli tries a few times to escape; but on one attempt, Bennish stops her. He has come to believe this isn’t so bad. He’s a better person, and he likes it. Seeing this, Alli is starting to believe it too.
Time passes, and Alli starts to change. She’s calmer. Happier. The time comes to be released, and Bennish offers for Alli to come live with him. She’s a bit taken by how nice their new home is, and it was already furnished; but then she notices something on the desk. An ID card for Conrad Bennish. No Junior. The Bennish she has come to know is the native version of that world - an assistant counselor at the facility she was placed in. She hadn’t noticed because they were never placed in a “cell” together; they always sat in a ring of chairs where everyone appeared equal; she always found him already in the recreation areas before she got there and never gave it much thought.
So the question it comes down to. The new person that Alli has become - is this the person she wants to be, or will she revert to her old self now that the vacation is over and it’s time to go home?
I would need to think a little more on a B plot to give Reese and Gibbs something to do (most likely focused on them trying to save Alli but finding only our Bennish instead), but we have our story foundation now. I did not intend it to be when we started, but this turned into a kind of sideways look at “Post Traumatic Slide Syndrome”.
Of course, the above is not a completed story - it’s the product of maybe an hour’s thought in an attempt to solve the puzzle you presented. But it has potential.