By ROTS, the two have come to realize that they may even have to go against their own morals and the Code, to stop the Sith.

Right, but I am not talking about them killing Sith, I am talking about them letting each other come to harm. In the book, Obi-Wan and Yoda are talking about Anakin, and how he is a fiercely loyal friend -- to the point where he is so attached to those he loves and cares about that he will go against the Code to do things for them. Obi-Wan tells Yoda that while he would sacrifice Yoda's life without thinking about it, if the need arose -- as he should, Yoda affirms, saying that he would do the same -- Anakin would not. This fierce attachment is a concern to them.

Take care,
Sojourn