I have to admit, I don't see it that way. I think more people will see it just as
@Hatmatter stated, she is upset that Paul is not going to be a monogamist with her as his solo partner.
In fact, in the lead up to this film, I recall they did interviews with Zendaya who expressed similar sentiments and how women should be more empowered, that this film would show more equalization for woman. Part of that is showing that she is not some appendage of Paul, but that if she is important than he needs to have her as his equal...not some concubine.
In the movie I definitely got that vibe as well. He's all about her during the main movie, but when he chooses the alliance via marriage, she's upset that he's trying to spurn her as not being equal in that way, and leaves.
I could be wrong, but I didn't get the message that this was her disagreeing with his messianic ascension in any way from watching the film and seeing her run off (upset running off at that) into the desert at the end.
I like the film, but I don't really see it representing what you are saying it is with Chani and Paul. If anything it shows Paul as resigning himself to his fate after fighting futilely against it, submitting to his desire for revenge and survival instead.