Perhaps Gus never pulled the trigger himself, but he is responsible for setting up the deaths of countless people. Yes, many are bad guys, but his only interest is in business. His guy screwed up, in his eyes. He didn't prevent Gale from dying, so all he had ever done, every moment of loyalty is out the window. Hey, maybe he could run for President. This is a really tense episode where Gus the practical man simply decides to let the boys continue their work. I mean, what does he have to lose by going along with Walter and Jesse? As long as they cook while he looks for other options, his business goes on.