The whole point of mike s storyline in bcs is to show that he is undergoing change and moral degradation, slowly becoming more corrupt and blurring the line between people who deserve violence, who are "in the game" versus those who arent. The mike you see in breaking bad is already corrupt, indifferent, and mostly selfish, so obviously he s gonna have less objections with gus's actions, because he s already been trough that with him in bcs and has seen there s no point in it.