That is a pretty bad reason to murder billions of people. Honestly, it makes more sense if Paul and Leto just screwed up, or where just being lead to turn Duncan into what he becomes. Paul and Leto were both way too sure of their visions. Paul would keep saying the future was always changing, but apparently Leto didn't get he memo, becuase he acts like only the "golden path" is the right choice. Besides which, how many planets are they supposed to colonise? The empire in Paul's day already had a huge number of habitable planets with people on them. Paul killed trillons and actually lowered the number of planets the empire had that could support life, so he wasn't following the "golden path".
In the end, its all BS. I just read it as Paul being to arrogant and wrongly believeing that his vision was the only right choice, and Leto was the same way, he just took it way too far. I guess you could say that Leto was partially responsible for saving humanity (because of his constant ressurection of Duncan Idaho) and maybe that was where his visions were actually leading him, but in the end he didn't do what he thought he was doing. His "golden path" was just a false trail, it was Duncan's evolution that really saved humanity. Thats weird, but makes a lot more sense than murdering billions of people to make them pointlessly migrate because of no real reason outside of confusing writing (Spreading out to save themselves is just kind of stupid, they were already fairly spread out, and the machines had all the time in the universe to find them and kill them all anyway). Also, that still doesn't explain why they needed to have people who were immune to people with visions, but I'm just going to accept that it happened and might make sense somehow.
Also, talking about the jihad, if Paul hadn't controlled the spice, the fremen would have been massacured by more powerful forces. All he had to do to stop them was not threaten the spice and not tell them how to do it (I think he's the one who learned how the spice could be destroyed I don't think the fremen had any idea befoire he came along). They were good fighters, but the empire/spacing guild was more than capable of killing hem all and leaving the spice intact, if Paul hadn't been their to threaten them. Plus, Paul was the one who riled them up. If he hadn't shown up, all the Freemen ould have done was continue Kynes plan.
It seems like I'm really not a fan of this stuff, but I love the Dune series. I just don't think parts of the overall story were done very well.