Sebastian wanted to say yes and tell him that the man had no other choice, but if he did say that, he had a feeling that Atlas would blow a fuse.
Additionally, before he leaves, he wants Atlas and him to be on good ground, not in a terrible dispute, because, at the end of the day, he truly can't guarantee that he will come back.
Sebastian responded in a way Atlas would want to hear: "I know that you're willing to be by my side and protect me, but how would you expect me to feel if something happens to you?"
Sebastian covered the man's mouth upon seeing the lips begin to move and completed the last words he wanted to say, "I know you don't like to hear what I have to say, but please do this for me. I'm not asking you to stay because I think you're weak or anything like that."