I think it's more that Walt and Jesse are causing more problems than they're worth. The meth is good and the reason Gus is at the top of the game right now. Anyone can cook meth, but not anyone can cook THAT kind of meth. He needs THAT meth in order to stay at the top, but he doesn't give a fuck who's cooking it. When Jesse and Walt are causing so many problems, they need to be dealt with. I don't think the problem was who they killed, but how many and how they did it. When you're leaving bodies in the streets it brings the police out, snooping around. That's why Mike kept telling Walt, "Get your fucking car fixed, idiot."
The dynamic between Gus and Walt is going to be interesting in season four. I always felt Gus liked Walt because of the circumstance. He knew Walt was smart and he knew his intentions for doing this weren't selfish, so that gave him an incentive to do business with him. When things started getting hectic, Gus made a play and gave him an assistant with the intention of the assistant taking over. The question is if Gus put Gale in place before with the intention of him taking over when Walt got too sick to cook or when he started causing too many problems. I don't think that was the case immediately, because if it was, he wouldn't have let Jesse be allowed into the fold. It was only AFTER everything goes down that he insists that Gale be Walts assistant with his secret intentions being to kill Walt as soon as Gale learns the recipe. Now that Walt knows what Gus is/was up to, it's going to be interesting to see how they react to one another.
