During the duel we hear the voice of the RM telling / showing Paul to be killed by Jamis. It is not clear to me: Why did she suggest that to him, and why of course did he refuse follow her suggestion? The RM seems to be a double agent; it feels like that she is using these prophecies to realize her own plan.
The RM was speaking metaphorically:
“Paul Atreides must die… for Kwisatz Haderach to rise.”
In simple terms, the fall of his father’s House is very much the central conflict and core narrative arc of Pt. 1. The film begins with Paul having visions of his family’s army lying scattered and dying, and it ends with that horror coming to pass. As Chani, the girl of Paul’s dreams, says, this is only the beginning of the story. Or if you want to get technical, it’s about half of it.
This duel is the significant turning point in Paul’s dawning awareness about his place in the universe. Prior to the film’s conclusion, he’s been unsure of how to interpret and accept his “dreams,” or visions, of what might be. After this point, there is little doubt about his path forward. He accepts this and then declares “my road leads into the desert.”
Paul Atreides has died. He has become something more.