However it ultimately turns out, they're going to have Chani take an active role in her fate. With Paul refusing to have a child with Irulan, and since she's otherwise nowhere to be found in the novel, I'm thinking Jessica is going to briefly show up from Caladan, track Chani down in the desert, and ultimately convince her to reunite with Paul for the greater good (and to save the all-important Atreides bloodline for the Sisterhood), even knowing it will lead to her death if she does.
As for destroying Paul's reputation... depends on if Legendary's willing to go for an R rating, and how hard an R at that. This is going to have to be 'show, not tell.' We're going to have to see the Fremen offworld (and I mean actually see, no cutting away like Star Wars) doing some absolutely diabolical war crime *@#% at a level that will undoubtedly draw parallels to current/recent real world events. And then drop the 61 billion figure (add a zero?) and make it crystal clear, beyond dispute, that Paul not only knows about all these events but signed off on them. And do that at the very start of the film, as if to challenge the audience: "You sure you want to see how all this ends? We'll tell you right here and now, there's no happy ending... at least, not one where Paul lives."