The Voth weren't villains. They wanted to be left alone, with their mythology intact. And they were also vastly more powerful than Voyager. There could ne no "civil war" because the information was retracted, and the population was fed bullshit, just like us.
They were pretty adversarial. Minister Odala would have had Voyager destroyed and the crew imprisoned had Gegen not backed down. Not to mention their generally racist attitude to non-saurians. It's also implied in the episode that there are other people like Gegen who believe the distant origin theory. Why not have the voth as villains but also Voyager could get help from a group of rebels or some other type of breakaway group. Of course there could be a civil war, a government as draconian as the Voth would not be without it's detractors.
Distant origin was worthy of a follow up because we learn there was this entire civilisation of Humanoid dinosaurs living on earth 65 million years ago. It's a cool idea and I would like to have seen more of it. Not sure why that is such a problem for you.