https://dune.fandom.com/wiki/Muad%27Dib%27s_Jihad
Among relatively sophisticated fans of Dune, it is widely accepted that Paul Atreides is not the hero of the story, that he isn't a "white savior," and that Frank Herbert intended the story as a warning against the kind of "charismatic leadership" that Paul engages in (Herbert said so himself!). But I would take the point further, and suggest it might well have been better, all things considered, if Paul and his Fremen rebellion had been crushed by the Harkonnens and the Emperor. It's a radical reinterpretation of the series. But I think there is a strong case for it. Here's why:
NOTE: Spoilers for the Dune series follow. Yes, SPOILERS:
1.Paul's Fremen Jihad leads to the death of 61 billion people (mostly innocent civilians), the "sterilization" of 90 inhabited worlds, and severe repression throughout the human-inhabited known universe (see link above). As one character in Dune Messiah (book 2 in the series) points out, Hitler's Holocaust (with its death toll of "merely" 6 million) seems insignificant by comparison. It takes a lot to outweigh that. And the putative benefits of the Paul's victory don't even come close.
It is true that Paul does succeed in liberating the Fremen from horrible Harkonnen oppression. But the new regime is only modestly better for them, as a high percentage of the male Fremen population ends up getting killed or maimed while fighting in the Jihad (this too is noted in Dune Messiah). In any event, any benefit to the Fremen of Arrakis is greatly outweighed by the cataclysmic harm inflicted on the populations of almost every other inhabited world (Caladan excepted, because Jessica wisely prevented the Fremen from establishing a presence there).
Had the Emperor and the Harkonnens prevailed, they would likely have established a regime similar to the status quo ante at the start of Dune. Very bad for the Fremen and the people living on the Harkonnen home world of Giedi Prime (which is a brutal dictatorship). But most of the rest of the Empire enjoys broad autonomy, a relatively high standard of living, and considerable freedom, so long as they don't openly challenge imperial authority. At the very least, the Corrino emperors don't commit mass murder on anything even remotely approaching the same scale as Paul's Jihad. The Great Houses of the Landsraad constrain imperial power, and keep it from degenerating into tyranny.
In the book, Baron Harkonnen has a plot to put his nephew Feyd Rautha on the imperial throne. If it were to succeed (which could happen in the event of Paul's defeat), a Harkonnen dynasty would likely be more repressive than the Corrinos. But such a success seems unlikely, as the Baron faces long odds, and Feyd Rautha is nowhere near competent enough. Even if the worst happens and Feyd does become emperor, his brutality would still be constrained by many of the same factors as those limiting the Corrinos. Unlike Paul, he would not have an ideologically fanatical army capable of perpetrating mass murder throughout the universe. Nor would he even necessarily want to, if he could. The Harkonnens are cruel and selfish. But they seem interested mainly in increasing their power and wealth, not transforming the universe to fit their ideology. A Harkonnen-ruled empire would be very bad. But nowhere near as much as Paul's Jihad.
The standard "justification" for Paul's decisions is that the Jihad was, in the long run, necessary to produce his son Leto II's "Golden Path," which in turn led to the "Scattering" which saved the human race from catastrophe. I won't go into all the details of this, which would require delving deep into subsequent books in the series. I will only say that this scenario requires accepting the accuracy of Paul and Leto II's visions at face value. Conveniently, those visions, justify giving them absolute power! Moreover, the idea that horrific mass murder is necessary to achieve a greater good is one normally associated with communist and Nazi totalitarians. It seems unlikely that Herbert (who, let us recall, wrote the series as a warning against fanaticism and charismatic leadership) actually meant to endorse this kind of idea. To the contrary, it seems more likely that Paul and Leto's prescience is, in signifcant part, delusional - much like the delusions that motivated Hitler (to whom Paul is explicitly compared in Dune Messiah!), Stalin, Mao, and other mass-murdering ideologues in our own history.
Matters might have been very different if Duke Leto I had somehow achieved a conventional victory over the Harkonnens and the Emperor before Paul could become the Fremen leader, and set out on the path to Jihad. In that event, Paul's destiny might have been very different, and the Atreides would likely have proved to be more benevolent (or at least less bad) rulers of Arrakis than the Harkonnens. But, that's not the direction in which Herbert takes the plot.
More generally, the Atreides (including Paul) are far nicer and more sympathetic people than the Harkonnens (Many of whom are borderline psychopathic) and the Emperor. But personally nice people who promote a horrific ideology that justifies mass murder can do more harm than cruel and venal people whose main goal is just to promote their narrow self-interest. History offers many examples to back up that point.
When I first read the book - and even now - I sympathize with Paul and his friends on an emotional level. They have many personal virtues, while the Harkonnens have none and the Corrinos not much more. But, rationally, the Emperor and the Harkonnens were still the lesser evil in this conflict, at least once Paul becomes the charismatic despot of the Fremen.
