I think you're forgetting the order of events here.
When they first meet Gus, Gus wants Walt, but not Jesse. Walt goes to bat for Jesse to bring him on board.
Later, Jesse has a dispute with two street-level dealers after they execute that kid. In one of the show's more unbelievable moments, Gus tells everyone to just get along.
Jesse then proceeds to go after the two dealers himself. Walt saves his ass. Jesse is on the run, and is as good as dead if Gus catches him. Gus decides to just replace both of them with Gale, and Walt is about to be executed, but he manages to get Gale's location to Jesse, who does what needs to be done, saving both of their asses.
It was only after Gale was dead that Gus decided he would rather kill Walt and keep Jesse alive, probably because Jesse was easier to manipulate.
If things had gone differently, and Mike had just shot Walt in the lab at the end of Season 3, Jesse would have been dead within a few days. On the other hand, if Walt had just allowed Jesse to be gunned down by those dealers, I don't think Gus would have had him killed.