I think Denis will try to contain Alia to the Messiah story only, and maybe end with her ascension and an open cautionary ending that leaves audiences to question if what Paul did was ultimately the right path. Denis’ Dune trilogy is about Paul’s arc after all, so I feel like he won’t focus on Alia beyond her actions as connected to Paul and the plot of Messiah. Obviously that means a lot of development that introduces what happens to her after Messiah will be cut out.
As for the weird stuff in the books the article points out, Denis will probably leave them out altogether; like making Hayt more of a trusted adviser only and removing the incest stuff.