Mr. Atkin was faced with a difficult situation. He had to choose between his cuntry, joining with every other American in seeking quick justice for the murder of the president, and seeing that justice was received in the right fashion. In the beginning of the film, he was on the side of quick justice. He was scared; he did not want to jump into the muck that the trial would bring. Eventually though, he saw that how so-called justice was being sought was not the "American" way. The trial was not by any means unprejudiced.
Mrs. Surratt and the others were facing criminal charges. The Constitution states that, "The Trial of all Crimes, except in Cases of Impeachment, shall be by Jury...." They faced a Military court. They were civilians not soldiers. They did not have an impartial jury. The list of injustice of the trial goes on and on. Mrs. Surratt was seen as guilty from the time her home was searched. We will never know for certain of her involvement in the conspiracy because she was not given a proper trial. I believe Mr. Atkin was doing his job as a lawyer, living up to the oath he took. If this trial was given special privileges what was to stop trials of the future of not taking the same path.
As for Mrs. Surratt's moral compassion, she was trying to protect her son. Many other parents would do the same thing for their children. She was strong in her faith.
As I see it, John Surratt believed that by staying away he was protecting his family. Obviously he was wrong. But who could foresee the events that would take place. America had never seen a trial or hysteria like that taking place after the war and Lincoln's death. It was an unstable time and everyone was terrified.