They were saying Wyll has to kill Karlach as a starting goal.
But Wyll could decide to not kill Karlach. Meaning Wyll has a big fork in the path early on. Good Wyll or Bad Wyll, player's choice.
Or at least that's what I understood from watching the PFH. Maybe I misunderstood something; I don't know.
You got it right. Wyll can choice not to kill Karlach (as the player character) or be convinced not to kill Karlach (as a companion).