I am partway through Dune Messiah, and it's apparent to me that Paul (and perhaps Frank Herbert) does not believe he is in control of his "Jihad." Why could he not just command his forces to stop?
If the logic behind this is later revealed toward the end of the book, please don't spoil it for me - just say so and obfuscate the rest of the answer. Thanks.
Without going into massive detail, it's because he's being swept along by (or, arguably, surfing) the tides of history. A history that had a lot more directing it to it's current course than just him and his actions. He was not just the culmination of the Bene Gesserit breeding program, but the man who stood at the focal point of a LOT of sociocultural meddling. (Much of it you've seen here, such as the Missionaria Protectiva's planting of the prophecy of a messiah.. But there is a lot more that hasn't been explained yet.)
Due to his prescience, he has some ability to see where changes can direct the flow of history somewhat.. But history itself is like a massive tidal wave; the best he can hope to do is channel it into a desired path; stopping it is simply not possible -- it has too much inertia by this point in the story. He's not choosing how he wants the universe to be, but, rather, steering it like an almost out-of-control ship running before a massive storm; he chooses the best of the options he can see, with his limited vision. (At one point he describes the view of time as having hills and valleys; depending on where he is at any given point, how far he can see if often very limited.)
Since you ask why he doesn't just order them to stop.. That comes up early in the book:
“Chani, beloved,” he whispered, “do you know what I’d spend to end the Jihad—to separate myself from the damnable godhead the Qizarate forces onto me?”
She trembled, “You have but to command it,” she said.
“Oh, no. Even if I died now, my name would still lead them. When I think of the Atreides name tied to this religious butchery …”
“But you’re the Emperor! You’ve—”
“I’m a figurehead. When godhead’s given, that’s the one thing the so-called god no longer controls.” A bitter laugh shook him. He sensed the future looking back at him out of dynasties not even dreamed. He felt his being cast out, crying, unchained from the rings of fate—only his name continued. “I was chosen,” he said. “Perhaps at birth … certainly before I had much say in it. I was chosen.
Keep reading, tho; he (and other characters) spend a good deal of time speculating on this very issue, here, and thru the rest of the books.
Some of this will become more clear in the next book. By "choosing" to take the mantle of Messiah in dune, mind you he's a 15 year old child still reeling from the death of his father and the desire for revenge so he isn't really fully cognizant of what that choice will ultimately mean, he sets a path for him self that he no longer truely controls. By taking that religious mantle and fulfilling the fremen prophesy he become diefied in his own lifetime and any attempts to change the path that was set when he chose revenge are viewed as test by the living god. Jessica knows the dangers inherent in that path but is unable to prevent Paul from taking it when they first encounter stilgar.
By the time you get through children of dune you'll get to see the path that leads humanity out of the genocide Paul creates, a path that Paul's knows he must take but is unwilling to make the sacrifice needed to accomplish it.
It is easy to start a war and it is easy to be popular and in command while the war you have ordered is going on and the army you command is winning. When you tell a winning army to stop chances are high that will be the end of your leadership. The more they think you are a spiritual leader the more they might think you were a false prophet after that.
